Diagnosis and treatment of autoimmune diseases

ABSTRACT

The invention relates generally to the field of autoimmunity. More specifically, the invention relates to compositions and methods for the diagnosis, prevention, and treatment of human leukocyte antigen (HLA)-associated autoimmune diseases, and in particular HLA-B27-associated autoimmune diseases.

INCORPORATION BY CROSS REFERENCE

This application claims priority from Australian provisional patent application number 2013902435 filed on 1 Jul. 2013, the entire content of which is incorporated herein by cross-reference.

TECHNICAL FIELD

The invention relates generally to the field of autoimmunity. More specifically, the invention relates to compositions and methods for the diagnosis, prevention, and treatment of human leukocyte antigen (HLA)-associated autoimmune diseases, and in particular HLA-B27-associated autoimmune diseases.

BACKGROUND

A substantial number of autoimmune diseases in mammals are associated with the expression of specific major histocompatibility complex (MHC) subtype(s). For example, spondyloarthropathies are a group of inflammatory autoimmune diseases associated with human leukocyte antigen B27 (HLA-B27) expression. Spondyloarthropathies affect the sacroiliac joints, axial skeleton, and, to a lesser degree, peripheral joints and certain extra-articular organs. Common spondyloarthropathies include ankylosing spondylitis (AS), reactive arthritis (RA) (also known as Reiter's syndrome), psoriatic arthritis, undifferentiated spondyloarthropathy, and juvenile onset spondyloarthropathy (collectively termed the B27 diseases). A significant proportion of patients affected by spondyloarthropathies develop anterior uveitis, an autoreactive inflammation localized primarily to the anterior segment of the eye. Spondyloarthropathies and anterior uveitis appear to be triggered by certain bacteria, and are particularly prevalent in HLA-B27 positive individuals. For example, ankylosing spondylitis (AS) has a greater than 90% correspondence with the expression of HLA-B27.

The diagnosis of spondyloarthropathies and anterior uveitis relies predominantly on clinical and radiological criteria which are often unreliable and misdiagnosis is common. Treatments consist primarily of symptom-relieving drugs which have minimal effect on the underlying causes of the disease. Furthermore, effective preventative treatments for spondyloarthropathies and anterior uveitis are virtually non-existent.

There is a need for improved agents and methods for the treatment and/or prevention of HLA-associated diseases such as spondyloarthropathies and anterior uveitis. A need also exists for improved agents and methods to diagnose these diseases and identify individuals predisposed to developing them.

SUMMARY OF THE INVENTION

In a first aspect, the invention provides an isolated polypeptide comprising a sequence of at least six amino acid residues, wherein said sequence shares at least 65% sequence homology with:

(a) a mammalian small leucine-rich repeat protein/proteoglycan (SLRP) polypeptide sequence; and

(b) a polypeptide sequence from an infectious microorganism,

wherein said SLRP is selected from lumican, opticin and keratocan.

In one embodiment of the first aspect, the sequence shares 75% with the mammalian SLRP polypeptide sequence and the polypeptide sequence from the infectious microorganism.

In one embodiment of the first aspect, the sequence shares 80% with the mammalian SLRP polypeptide sequence and the polypeptide sequence from the infectious microorganism.

In one embodiment of the first aspect, the sequence shares 85% with the mammalian SLRP polypeptide sequence and the polypeptide sequence from the infectious microorganism.

In one embodiment of the first aspect, the sequence shares 90% with the mammalian SLRP polypeptide sequence and the polypeptide sequence from the infectious microorganism.

In one embodiment of the first aspect, the sequence shares 95% with the mammalian SLRP polypeptide sequence and the polypeptide sequence from the infectious microorganism.

In one embodiment of the first aspect, the isolated polypeptide is 12 amino acid residues or less in length.

In one embodiment of the first aspect, the isolated polypeptide is nine amino acid residues in length.

In one embodiment of the first aspect, the infectious microorganism is a species from genus Chlamydia or Aspergillus.

In one embodiment of the first aspect, the infectious microorganism is Chlamydia trachomatis.

In one embodiment of the first aspect, the infectious microorganism is Aspergillus nidulans.

In one embodiment of the first aspect, the polypeptide sequence of (b) comprises SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 36, SEQ ID NO: 37, or SEQ ID NO: 38.

In one embodiment of the first aspect, the polypeptide sequence of (a) comprises residues 222-275 of the amino acid sequence set forth in SEQ ID NO: 1.

In one embodiment of the first aspect, the polypeptide sequence of (a) comprises residues 222-247 of the amino acid sequence set forth in SEQ ID NO: 1.

In one embodiment of the first aspect, the polypeptide sequence of (a) comprises residues 222-241 of the amino acid sequence set forth in SEQ ID NO: 1.

In one embodiment of the first aspect, the sequence of at least six amino acid residues comprises SEQ ID NO: 2 (KRFNALQYL).

In one embodiment of the first aspect, the sequence of at least six amino acid residues consists of SEQ ID NO: 2 (KRFNALQYL).

In one embodiment of the first aspect, the sequence of at least six amino acid residues comprises a variant of SEQ ID NO: 2 (KRFNALQYL) comprising at least one amino acid substitution.

In one embodiment of the first aspect, the variant is selected from the group consisting of KRFNALQCL (SEQ ID NO: 3) or KRFNALQLL (SEQ ID NO: 4), or a fragment thereof.

In one embodiment of the first aspect, the sequence of at least six amino acid residues comprises a fragment of SEQ ID NO: 2 (KRFNALQYL).

In one embodiment of the first aspect, the fragment is selected from a sequence set forth in any one of SEQ ID NOs: 9-17.

In one embodiment of the first aspect, the polypeptide comprises a fragment of KRFNALQCL (SEQ ID NO: 3) or KRFNALQLL (SEQ ID NO: 4) selected from a sequence set forth in any one of SEQ ID NOs: 18-29.

In one embodiment of the first aspect, the sequence of at least six amino acid residues comprises SEQ ID NO: 34 (LQYLRLSHN).

In one embodiment of the first aspect, the sequence of at least six amino acid residues consists of SEQ ID NO: 34 (LQYLRLSHN).

In one embodiment of the first aspect, the polypeptide sequence of (a) comprises residues 264-315 of the amino acid sequence set forth in SEQ ID NO: 30.

In one embodiment of the first aspect, the sequence of at least six amino acid residues comprises SEQ ID NO: 31 (LQNNLIETM) or SEQ ID NO: 35 (QLEDIRLDG).

In one embodiment of the first aspect, the sequence of at least six amino acid residues consists of SEQ ID NO: 31 (LQNNLIETM) or SEQ ID NO: 35 (QLEDIRLDG).

In one embodiment of the first aspect, the polypeptide sequence of (a) comprises residues 264-315 of the amino acid sequence set forth in SEQ ID NO: 32.

In one embodiment of the first aspect, the sequence of at least six amino acid residues comprises SEQ ID NO: 33 (LQNNLIETI).

In one embodiment of the first aspect, the sequence of at least six amino acid residues consists of SEQ ID NO: 33 (LQNNLIETI).

In one embodiment of the first aspect, the binding affinity of said sequence of at least six amino acid residues to human leukocyte antigen B27 (HLA-B27) as measured by IC₅₀ value is less than about 500 nm.

In another embodiment of the first aspect, the binding affinity of said sequence of at least six amino acid residues to human leukocyte antigen B27 (HLA-B27) as measured by IC₅₀ value is less than about 100 nm.

In another embodiment of the first aspect, the binding affinity of said sequence of at least six amino acid residues to human leukocyte antigen B27 (HLA-B27) as measured by IC₅₀ value is less than about 50 nm.

In a second aspect, the invention provides a pharmaceutical composition comprising an isolated polypeptide of the first aspect.

In one embodiment of the second aspect, the pharmaceutical composition further comprises a pharmaceutically acceptable carrier, diluent or adjuvant.

In one embodiment of the second aspect, the pharmaceutical composition is a preventative or therapeutic vaccine.

In a third aspect, the invention provides a method for preventing or treating an HLA-associated autoimmune disease in a subject, the method comprising administering to the subject a therapeutically effective amount of an isolated polypeptide of the first aspect, or a pharmaceutical composition of the second aspect.

In a fourth aspect, the invention provides a method for determining a predisposition to developing an HLA-associated autoimmune disease in a subject, the method comprising:

contacting a biological sample from the subject with a polypeptide of the first aspect; and

detecting the presence or absence of an immune cell or antibody specific for said polypeptide in the biological sample,

wherein detection of said immune cell or antibody is indicative of a predisposition to developing the disease.

In a fifth aspect, the invention provides a method for diagnosing an HLA-associated autoimmune disease in a subject, the method comprising:

contacting a biological sample from the subject with an isolated polypeptide of the first aspect; and

detecting the presence or absence of an immune cell or antibody specific for said polypeptide in the biological sample,

wherein detection of said immune cell or antibody is indicative of a predisposition to developing the disease.

In one embodiment of the fourth or fifth aspect, the method comprises the additional step of determining the human leukocyte antigen type (HLA-type) of the subject.

In one embodiment of the fourth or fifth aspect, the detecting comprises:

(i) analysing antibody binding by enzyme-linked immunosorbent assay (ELISA),

(ii) analysing cell proliferation,

(iii) analysing cytokine synthesis, or

(iv) analysing cell surface marker expression.

In one embodiment of the fourth or fifth aspect, the immune cell is a CD4⁺ T lymphocyte or a CD8⁺ T lymphocyte.

In one embodiment of the third, fourth or fifth aspect, the HLA-associated autoimmune disease is an HLA-B27-associated autoimmune disease.

In one embodiment of the third, fourth or fifth aspect, the HLA-associated autoimmune disease is a spondyloarthropathy or anterior uveitis.

In one embodiment of the third, fourth or fifth aspect, the spondyloarthropathy is selected from the group consisting of ankylosing spondylitis, psoriatic arthritis, undifferentiated spondyloarthropathy, juvenile onset spondyloarthropathy, enteropathic arthritis, arthritis mutilans, reactive arthritis (Reiter's syndrome), reactive arthritides, sacroiliitis, spondylitis of inflammatory bowel disease, Crohn's disease associated with spondyloarthropathy, whipple disease, and Behcet disease.

In one embodiment of the third, fourth or fifth aspect, the anterior uveitis is acute anterior uveitis.

In one embodiment of the third, fourth or fifth aspect, the anterior uveitis is chronic anterior uveitis.

In a sixth aspect, the invention provides an antibody specific for a polypeptide of the first aspect.

In a seventh aspect, the invention provides an isolated polypeptide of the first aspect or a pharmaceutical composition of the second aspect, for use in preventing or treating an HLA-associated autoimmune disease.

In an eighth aspect, the invention provides a use of an isolated polypeptide of the first aspect for the preparation of a medicament for preventing or treating an HLA-associated autoimmune disease.

In one embodiment of the seventh or eighth aspect, the HLA-associated autoimmune disease is an HLA-B27-associated autoimmune disease.

In one embodiment of the seventh or eighth aspect, the HLA-associated autoimmune disease is a spondyloarthropathy or anterior uveitis.

In one embodiment of the seventh or eighth aspect, the spondyloarthropathy is selected from the group consisting of ankylosing spondylitis, psoriatic arthritis, undifferentiated spondyloarthropathy, juvenile onset spondyloarthropathy, enteropathic arthritis, arthritis mutilans, reactive arthritis (Reiter's syndrome), reactive arthritides, sacroiliitis, spondylitis of inflammatory bowel disease, Crohn's disease associated with spondyloarthropathy, whipple disease, and Behcet disease.

In one embodiment of the seventh or eighth aspect, the anterior uveitis is acute anterior uveitis.

In one embodiment of the seventh or eighth aspect, the anterior uveitis is chronic anterior uveitis.

BRIEF DESCRIPTION OF THE DRAWINGS

Preferred embodiments of the invention will now be described, by way of example only, with reference to the accompanying figures wherein:

FIG. 1 provides fluorescence microscopy images showing lumican expression in human iris epithelial cells (1A and 1E), iris tissues (1B and 1F), and synovial tissues (1C-1D, 1G-1H). Original magnification ×100 (1A, 1E) and ×400 (1B-1D, 1F-1H);

FIG. 2 is a graph showing the results of an Elispot assay measuring IFN-γ responses to HLA B27-binding peptides in peripheral blood mononuclear cells (PBMC) of two patients with acute uveitis (b27028 and b27030) and two control subjects (c002 and c005). X-axis—Nos. 1-4: peptide mixtures corresponding to sets 1-4 of Table 25; No. 5: EBV peptide from Table 25; No. 6: recombinant human lumican; No. 7: negative control (complete RPMI); Y-axis—ratio of spot-forming units (SFU's) (sample vs negative control media). Negative control is by definition 1.0 on the Y-axis. PHA is not shown though all cells displayed a strong response to it. All peptides were made to final concentrations of 5 μg/mL each and recombinant human lumican was used at a final concentration of 2.5 μg/mL;

FIG. 3 is a graph showing averaged results of an Elispot assay measuring IFN-γ responses after administration of lumican protein (2.5 μg/mL) to PBMC of HLA B27 positive patients and PBMC of controls. IFN-γ responses were compared to control and patient PBMC administered only media. X-axis: sample. Y-axis—ratio of spot-forming units (SFU's) (sample vs negative control media). Negative control is by definition 1.0 on the Y-axis;

FIG. 4 is a graph showing the results of an Elispot assay measuring IFN-γ responses to six different HLA B27-binding peptides in two patients with acute uveitis (b27004; b27007) and two control subjects (c001 and c004). X-axis: sample/peptide administered. Peptide 1: KRFNALQYL (Lumican) Peptide 2: LQNNLIETI (Keratocan/Opticin); Peptide 3: LQYLRLSHN (Lumican); Peptide 4: QLEDIRLDG (Opticin); Peptide 5: PLNLRSIDL (Chlamydlia trachomalis); Peptide 6: ARKLLLDNL (Chlamydia trachomalis). Y-axis—ratio of spot-forming units (SFU's) (sample vs negative control media). Negative control is by definition 1.0 on the Y-axis;

FIG. 5 provides a series of graphs showing PBMC responses to stimulation with peptide mixtures or aggrecan peptide in an EliSpot assay. Interferon-gamma spot forming cells (IFNg SFC) per 2×10⁵ PBMCs are represented as mean+/−SD in duplicates. A positive response (*) to a peptide (or mixture) is defined by the mean SFCs>background +3SD. IFNg secretion was observed from PBMCs of 3 HLA-B27+AAU patients (A-C) but not from a HLA-B27—normal subject (D). X-axis—sample/peptide mix administered. Y axis—interferon-gamma spot forming cells (TFNγ SFC) per 2×10⁵ PBMCs are represented as mean+/−SD in duplicates;

FIG. 6 is a graph showing the results of an HLAB*2705 peptide binding assay using peptides derived from the human lumican protein. The binding score for each peptide is shown as a percentage relative to the binding of the positive control (X-axis). Peptide numbers are shown on the Y-axis and correspond to those listed in Table 22. The pass/fail threshold is indicated by the horizontal line at 45%;

FIG. 7 is a photographic image of a mouse administered peptides in accordance with the methods of the present invention; and

FIG. 8 is a graph showing the percentage of CD4+T cells in peripheral blood of HLAB27 patients specific for Chlamydia and Lumican peptides.

DEFINITIONS

As used in this application, the singular form “a”, “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a polypeptide” also includes a plurality of polypeptides.

As used herein, the term “comprising” means “including.” Variations of the word “comprising”, such as “comprise” and “comprises,” have correspondingly varied meanings. Thus, for example, a polypeptide “comprising” a sequence of amino acid residues may consist exclusively of that sequence of amino acid residues or may include one or more additional amino acid residues.

As used herein the term “plurality” means more than one. In certain specific aspects or embodiments, a plurality may mean 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, or more, and any integer derivable therein, and any range derivable therein.

The term “therapeutically effective amount” as used herein, includes within its meaning a non-toxic but sufficient amount of a compound or composition for use in the invention to provide the desired therapeutic effect. The exact amount required will vary from subject to subject depending on factors such as the species being treated, the age and general condition of the subject, the severity of the condition being treated, the particular agent being administered, the mode of administration and so forth. Thus, it is not possible to specify an exact “effective amount”. However, for any given case, an appropriate “effective amount” may be determined by one of ordinary skill in the art using only routine experimentation.

As used herein, the term “subject” includes any animal of economic, social or research importance including bovine, equine, ovine, primate, avian and rodent species. Hence, a “subject” may be a mammal such as, for example, a human or a non-human mammal.

As used herein, the terms “antibody” and “antibodies” include IgG (including IgG1, IgG2, IgG3, and IgG4), IgA (including IgA1 and IgA2), IgD, IgE, or IgM, and IgY, whole antibodies, including single-chain whole antibodies, and antigen-binding fragments thereof. Antigen-binding antibody fragments include, but are not limited to, Fab, Fab′ and F(ab′)2, Fd, single-chain Fvs (scFv), single-chain antibodies, disulfide-linked Fvs (sdFv) and fragments comprising either a VL or VH domain. The antibodies may be from any animal origin. Antigen-binding antibody fragments, including single-chain antibodies, may comprise the variable region(s) alone or in combination with the entire or partial of the following: hinge region, CH1, CH2, and CH3 domains. Also included are any combinations of variable region(s) and hinge region, CH1, CH2, and CH3 domains. Antibodies may be monoclonal, polyclonal, chimeric, multispecific, humanized, and human monoclonal and polyclonal antibodies which specifically bind the biological molecule.

As used herein, the terms “protein” and “polypeptide” each refer to a polymer made up of amino acids linked together by peptide bonds and are used interchangeably herein. For the purposes of the present invention a “polypeptide” may constitute a full length protein or a portion of a full length protein.

As used herein, the term “polynucleotide” refers to a single- or double-stranded polymer of deoxyribonucleotide, ribonucleotide bases or known analogues or natural nucleotides, or mixtures thereof.

As used herein, the term “kit” refers to any delivery system for delivering materials. Such delivery systems include systems that allow for the storage, transport, or delivery of reaction reagents (for example labels, reference samples, supporting material, etc. in the appropriate containers) and/or supporting materials (for example, buffers, written instructions for performing the assay etc.) from one location to another. For example, kits include one or more enclosures, such as boxes, containing the relevant reaction reagents and/or supporting materials. The term “kit” includes both fragmented and combined kits.

As used herein, the term “fragmented kit” refers to a delivery system comprising two or more separate containers that each contains a subportion of the total kit components. The containers may be delivered to the intended recipient together or separately. Indeed, any delivery system comprising two or more separate containers that each contains a subportion of the total kit components are included in the term “fragmented kit”. In contrast, a “combined kit” refers to a delivery system containing all of the components of a reaction assay in a single container (e.g. in a single box housing each of the desired components).

As used herein, an “MHC-associated autoimmune disease” encompasses any autoimmune disease that, in a given population of subjects, has an increased prevalence in subjects expressing a specific MHC allele or a specific combination of MHC alleles, compared to subjects that do not express that specific MHC allele or that specific combination of MHC alleles. It will be understood that an “MHC-associated autoimmune disease” as used herein includes, but is not limited to, an “HLA-associated autoimmune disease”.

As used herein, an “HLA-associated autoimmune disease” encompasses any autoimmune disease that, in a given population of human subjects, has an increased prevalence in subjects expressing a specific HLA allele or a specific combination of HLA alleles, compared to subjects that do not express that specific HLA allele or that specific combination of HLA alleles. It will be understood that an “HLA-associated autoimmune disease” as used herein includes, but is not limited to, an “HLA-B27 associated autoimmune disease”.

As used herein, an “HLA-B27 associated autoimmune disease” encompasses any autoimmune disease or condition that, in a given population of human subjects, has an increased prevalence in subjects that are homozygous for an HLA-B27 allele compared to subjects that are not homozygous for an HLA allele, and/or has an increased prevalence in subjects that are heterozygous for an HLA-B27 allele compared to subjects that do not express an HLA allele.

It will be understood that use the term “about” herein in reference to a recited numerical value includes the recited numerical value and numerical values within plus or minus ten percent of the recited value. Any description of prior art documents herein, or statements herein derived from or based on those documents, is not an admission that the documents or derived statements are part of the common general knowledge of the relevant art.

It will be understood that use of the term “between” herein when referring to a range of numerical values encompasses the numerical values at each endpoint of the range. For example, a polypeptide of between 10 residues and 20 residues in length is inclusive of a polypeptide of 10 residues in length and a polypeptide of 20 residues in length.

Any description of prior art documents herein, or statements herein derived from or based on those documents, is not an admission that the documents or derived statements are part of the common general knowledge of the relevant art.

For the purposes of description all documents referred to herein are hereby incorporated by reference in their entirety unless otherwise stated.

DETAILED DESCRIPTION

The present invention relates to the finding that certain proteins of infectious microorganisms induce autoimmune responses leading to the destruction of host cells and tissues. Without being limited to a particular mode of action, it is proposed that host immune cells and antibodies directed towards specific antigenic determinants in proteins of infectious microorganisms aberrantly recognise similar or identical antigenic determinants present in a specific host proteins identified herein. The abberant recognition of antigenic determinants in these host proteins instigates the destruction of cells and tissues in which they are expressed.

The present invention thus relates to the identification of antigenic determinants in proteins of infectious microorganisms that induce autoimmune responses against proteins of an infected host organism. The present invention also relates to the identication of antigenic determinants in host proteins targeted by cross-reactive immune responses arising upon infection/re-infection by certain microorganisms.

Some aspects of the present invention relate to polypeptides comprising region(s) of sequence homology shared by host proteins and proteins of infectious microorganisms. These region(s) of sequence homology are proposed to be responsible for the development of autoreactive immune cells and antibodies in subjects suffering from HLA-associated autoimmune diseases including spondyloarthropathies and anterior uveitis. The polypeptides may be incorporated into pharmaceutical compositions such as preventative and therapeutic vaccines.

Other aspects of the present invention relate to methods for preventing or treating HLA-associated autoimmune diseases (e.g. spondyloarthropathies and anterior uveitis) by administering polypeptides or compositions of the invention.

Assitional aspects of the present invention relate to methods for diagnosing or prognosing HLA-associated autoimmune diseases (e.g. spondyloarthropathies and anterior uveitis) by detection of immune cells or antibodies specific for polypeptides of the invention in, for example, a biological sample derived from a subject of interest.

Polypeptides and Polynucleotides Polypeptides

The invention provides polypeptides having sequence homology with at least one protein of an infectious microorganism and a small leucine-rich repeat protein/proteoglycan (SLRP) of a host organism susceptible to infection by the microorganism. The host may be any animal of economic, social or research importance including bovine, equine, ovine, primate, avian and rodent species. In certain embodiments the host may be a mammal. The mammal may be, for example, a human. The human may be positive for HLA-B27.

As contemplated herein “sequence homology” between two given sequences refers to the degree of sequence homology over the specific region defined by the sequences when optimally aligned.

Polypeptides of the invention share sequence homology with at least one protein of an infectious microorganism and at least one mammalian small leucine-rich repeat protein/proteoglycan (SLRP) expressed by a host susceptible to infection by the microorganism. Preferably, the host protein is lumican, opticin or keratocan.

It is postulated that the horseshoe-like shape of SLRPs such as lumican, opticin and keratocan may provide entry points for infectious microorganisms (e.g. bacteria). Furthermore, it is believed that differential keratin sulphate patterns in SLRPs such as lumican, opticin and keratocan occurring at different stages of development (e.g. infant vs adult) may be responsible, at least in part, for the increased susceptibility of specific age groups to spondyloarthropathies and/or anterior uveitis (e.g. the faster onset of juvenile spondyloarthropathies).

Polypeptides of the invention may share sequence homology with a mammalian lumican protein. The mammalian lumican protein may be a human lumican protein.

The human lumican protein may have the sequence set forth in SEQ ID NO: 1 (GenBank accession no. P51884), or a variant or a fragment thereof.

In certain embodiments, polypeptides of the invention may have sequence homology with a specific region of the human lumican protein. The region of the human lumican protein may be defined by residues 222-275 of the sequence set forth in SEQ ID NO: 1, or a fragment thereof. The region may be defined by residues 222-247 of the sequence set forth in SEQ ID NO: 1, or a fragment thereof. The region may be defined by residues 222-241 of the sequence set forth in SEQ ID NO: 1, or a fragment thereof. The region may be defined by the sequence set forth in SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 34, or a fragment thereof.

The human opticin protein may have the sequence set forth in SEQ ID NO: 30 (GenBank accession no. CAB53459), or a variant or a fragment thereof.

In certain embodiments, polypeptides of the invention have sequence homology with a specific region of the human opticin protein. The region of the human opticin protein may be defined by residues 264-315 of the sequence set forth in SEQ ID NO: 30, or a fragment thereof. The region may be defined by the sequence set forth in SEQ ID NO: 31, SEQ ID NO: 35, or a fragment thereof.

In certain embodiments, polypeptides of the invention have sequence homology with a specific region of the human keratocan protein. The human keratocan protein may have the sequence set forth in SEQ ID NO: 32 (GenBank accession no. AAC17741.1), or a variant or a fragment thereof. The region of the human keratocan protein may be defined by residues 71-91 of the sequence set forth in SEQ ID NO: 32, or a fragment thereof. The region may be defined by the sequence set forth in SEQ ID NO: 33, or a fragment thereof. Polypeptides of the invention share sequence homology with at least one host lumican protein. The polypeptide may share at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or greater than 95% sequence homology with the host SLRP protein such as, for example, a host lumican protein, a host opticin protein, or a host keratocan protein.

In certain embodiments of the invention, the polypeptide shares 100% sequence homology with a host SLRP protein (e.g. lumican, opticin or keratocan). Accordingly, a polypeptide of the invention may be identical to a host SLRP protein (e.g. a mammalian lumican, opticin or keratocan protein) or a fragment of a host SLRP protein (e.g. a fragment of a mammalian lumican, opticin or keratocan protein). Alternatively, the polypeptide may comprise a sequence that is identical to a host SLRP sequence (e.g. a mammalian lumican, opticin or keratocan protein sequence) or a fragment of a host SLRP sequence (e.g. a fragment of a mammalian host lumican, opticin or keratocan sequence).

Polypeptides of the invention share sequence homology with at least one protein of an infectious microorganism. It will be understood that an “infectious microorganism” as contemplated herein is a reference to a microorganism capable of establishing an infection in a host (e.g. a mammalian host). Non-limiting examples of infectious microorganisms from which the proteins may be derived include bacteria and fungi.

For example, in certain embodiments the protein is from a bacterium. Non-limiting examples include species of the genus Chlamydia (e.g. C. trachomatis, C. pneumoniae). Bacterial proteins to which polypeptides of the invention may share sequence homology include, but are not limited to, Chlamydia sp. fructose biphosphate aldolase protein (NCBI Reference Sequence: YP_002888714.1—SEQ ID NO: 5), OMP85 protein (Swiss-Prot: Q3KMCl—SEQ ID NO: 6), serine protease do-like protein (Swiss-Prot: P18584.2-SEQ ID NO: 7), 2-component regulatory system-sensor histidine kinase (NCBI Reference Sequence: NP_219980.1), hypothetical protein CT610 (NCBI Reference Sequence: NP_220127.1), or putative outer membrane protein C (NCBI Reference Sequence: NP_219924.1).

Non-limiting examples of bacterial peptides to which polypeptides of the invention may share sequence homology include those set forth in SEQ ID NO: 36, SEQ ID NO: 37, and SEQ ID NO: 38.

In other embodiments, the protein is from a fungus/yeast. Non-limiting examples include species of the genus Aspergillus (also known as Emericella) (e.g. A. nidulans/E. nidulans).

Fungal/yeast proteins to which polypeptides of the invention may share sequence homology include, but are not limited to, Aspergillus sp. uncharacterised protein (Swiss-Prot: Q5AR 12—SEQ ID NO: 8).

Polypeptides of the invention share sequence homology with at least one protein of an infectious microorganism. The polypeptide may share at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or greater than 95% sequence homology with the protein(s).

In certain embodiments of the invention, the polypeptide shares 100% sequence homology with protein(s) of an infectious microorganism. Accordingly, a polypeptide of the invention may be identical to at least one protein of an infectious microorganism or a fragment of at least one protein of an infectious microorganism. Alternatively, the polypeptide may comprise a sequence that is identical to at least one protein of an infectious microorganism or a fragment of at least one protein of an infectious microorganism.

It will be understood that the degree of sequence homology between a polypeptide of the invention and a host SLRP protein (e.g. lumican, opticin or keratocan) need not be identical to the degree of sequence homology between that polypeptide and protein(s) of an infectious microorganism, although such a possibility is not excluded.

Accordingly, a polypeptide of the invention may exhibit any of the aforementioned percentages of sequence homology with a host SLRP protein (e.g. lumican, opticin or keratocan) in combination with any of the aforementioned percentages of sequence homology with protein(s) of an infectious microorganism.

The percentage of sequence identity between two sequences may be determined by comparing two optimally aligned sequences over a comparison window. A portion of a sequence (e.g. a polypeptide of the invention) in the comparison window may, for example, comprise deletions or additions (i.e. gaps) in comparison to a reference sequence (e.g. a host or bacterial protein) which does not comprise deletions or additions, in order to align the two sequences optimally, or vica versa. A percentage of sequence identity may then be calculated by determining the number of positions at which an identical amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity.

Hence, in the context of two or more polypeptide sequences the percentage of sequence identity refers to the specified percentage of amino acid residues that are the same over a specified region when compared and aligned for maximum correspondence over a comparison window, or designated region as measured, for example, using one of the following sequence comparison algorithms or by manual alignment and visual inspection.

For sequence comparison, typically one sequence acts as a reference sequence to which test sequence(s) are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percentage of sequence homology for the test sequence(s) relative to the reference sequence, based on the program parameters.

Methods of alignment of sequences and/or the determination of sequence homology are known in the art and can be achieved conventionally using known computer programs including, but not limited to, CLUSTAL in the PC/Gene program (available from Intelligenetics, Mountain View, Calif.), the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the GCG Wisconsin Genetics Software Package, Version 10 (available from Accelrys Inc., 9685 Scranton Road, San Diego, Calif., USA).

A polypeptide of the invention may be of any length.

As will be recognised by the skilled addressee, a polypeptide sequence as exemplified herein may further include one, two, three, four, five or more than five additional amino acids immediately upstream (i.e. 5′) and/or downstream (i.e. 3′) of the exemplified polypeptide. The additional amino acid(s) may be selected from the group consisting of A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, Y or V.

The additional amino acid(s) may, for example, correspond to amino acids immediately upstream and/or downstream in the amino acid sequence of an SLRP protein (e.g. lumican, opticin or keratocan) of which the polypeptide is a constituent. Alternatively, the additional amino acids may not correspond to amino acids immediately upstream and/or downstream in the amino acid sequence of the protein from which the polypeptide is a constituent.

The skilled addressee will also recognise that one or more amino acids of a Jo polypeptide of the invention as exemplified herein may be deleted or substituted without necessarily reducing the immunogenic activity of the polypeptide.

In certain embodiments, polypeptides of the invention may be used to stimulate an immune response in a host. In other embodiments, polypeptides of the invention may be used to induce tolerance to an antigen in a host. In other embodiments, polypeptides of the invention may be used to detect the presence of immune cells and/or antibodies specific for the polypeptides in biological samples. Accordingly, a polypeptide of the invention may be of a length suitable for processing by host immune cells (e.g. antigen presenting cells) and subsequent binding to major histocompatibility (MHC) proteins.

In preferred embodiments, a polypeptide of the invention may comprise at least (or at least about) 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 20, 25, 30, 35, 40, 45, or 50 amino acids.

In other preferred embodiments, a polypeptide of the invention may comprise less than (or less than about) 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 20, 25, 30, 35, 40, 45, or 50 amino acids.

Accordingly, in some preferred embodiments a polypeptide of the invention may comprise (or comprise about) 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more than 30 amino acids.

In certain embodiments, polypeptides of the invention comprise less than 15 amino acids. In other embodiments, polypeptides of the invention comprise less than 12 amino acids. In some preferred embodiments, polypeptides of the invention comprise or consist of eight amino acids or nine amino acids. In other preferred embodiments, polypeptides of the invention comprise or consist of an amino acid sequence as set out in any of SEQ ID NOs: 2, 3, 4, 9-29, 31 or 33-40.

Polypeptides of the invention may be expressed as antigens by host immune cells. Typically, polypeptides of the invention introduced to host immune cells are processed and displayed on the cell surface bound to Major Histocompatibility Complex (MHC) proteins of the cell. The display of these antigenic determinants in association with the MHC proteins may elicit the proliferation of host immune cells including T-lymphocyte clones specific to the determinants. In humans, MHC proteins are Human Leukocyte Antigen (HLA) proteins.

A polypeptide of the invention may be of a length and/or conformation suitable for binding to an MHC class I protein (e.g. between about 6 and about 12 residues) and may comprise a hydrophobic residue at its C-terminus.

For example, a polypeptide of the invention may be of a length and/or conformation suitable for binding to a human MHC class I protein (e.g. any one or more of the HLA-A, HLA-B, HLA-C, HLA-D, HLA-E, HLA-F, or HLA-G subtypes).

In certain embodiments, the polypeptide is of a length and/or conformation suitable for binding to a human MHC class I protein associated with spondyloarthropathies and/or anterior uveitis (e.g. anterior acute uveitis). For example, a polypeptide of the invention may be of a length and/or conformation suitable for binding to an HLA-B protein (e.g. HLA-B2705, HLA-B1503), or an HLA-A protein (e.g. HLA-A0202, HLA-A2301, HLA-A2902).

In one embodiment, the polypeptide is of a length and/or conformation suitable for binding to HLA-B27. The polypeptide may be of a length and/or conformation suitable for binding to any HLA-B27 allele (e.g. HLA-B2701-HLA-B2728) including, but not limited to, HLA-B2705.

A polypeptide of the invention may be of a length and/or conformation suitable for binding to an MHC class II protein (e.g. between about 14 and about 24 residues).

For example, a polypeptide of the invention may be of a length and/or conformation suitable for binding to a human MHC class II protein (e.g. HLA-DM-Alpha, HLA-DM-Beta, HLA-DO-Alpha, HLA-DO-Beta, HLA-DP-Alpha1, HLA-DQ-Alpha1, HLA-DQ-Alpha2, HLA-DQ-Beta1, HLA-DR-Alpha, HLA-DR-Beta1, HLA-DR-Beta3, HLA-DR-Beta4 or HLA-DR-Beta5).

In certain embodiments, the polypeptide is of a length and/or conformation suitable for binding to a human MHC class II protein associated with autoimmune disease(s). For example, a polypeptide of the invention may be of a length and/or conformation suitable for binding to an HLA-DR protein (e.g. HLA-DR01, DR0404 and HLA-DR0405).

In one embodiment, the polypeptide is of a length and/or conformation suitable for binding to HLA-DR4. The polypeptide may be of a length and/or conformation suitable for binding to any HLA-DR4 allele (e.g. HLA-DR0401-HLA-DR0460) including, but not limited to, HLA-0401, HLA-DR0404 and HLA-DR0405.

Preferably, polypeptides of the invention bind to MHC proteins (e.g. HLA proteins) with high affinity. For example, the affinity of a polypeptide of the invention for a given MHC protein (as measured by IC₅₀) may less than about 500 nM, less than about 400 nM, less than about 300 nM, less than about 200 nM, less than about 100 nM, less than about 50 nM, less than about 40 nM, less than about 30 nM, less than about 20 nM, less than about 10 nM, or less than about 5 nM.

Polypeptides of the invention (including fusion polypeptides described in the subsection below entitled “Fusion polypeptides”) may be immunogenic polypeptides. For example, a polypeptide of the invention may comprise one or more epitopes capable of being recognized and bound by the immune cells and/or antibodies of an organism to which the polypeptide is administered. Preferably, the immune cells of the host organism capable of recognising and binding the polypeptides are T lymphocytes. In some embodiments, polypeptides of the invention are capable of inducing immunological tolerance.

Fusion Polypeptides

A polypeptide of the invention may be included as a component part of a longer amino acid sequence. For example, a polypeptide of the invention may be present within a fusion protein/fusion polypeptide wherein the polypeptide is linked with one or more amino acid sequences to which it would not be linked to in nature.

In this context it will be understood that a fusion polypeptide may comprise a plurality of polypeptides of the invention, such as where two polypeptides, three polypeptides, four polypeptides, or five polypeptides or more of the invention are present in a single fusion polypeptide. Any combination of polypeptides of the invention may be contemplated. In preferred embodiments a plurality of polypeptides may be selected such that the fusion polypeptide comprises polypeptides identified as comprising advantageous immunogenic responses in a given set of circumstances, as can be determined by the skilled addressee.

A fusion polypeptide comprising one or more polypeptide(s) of the invention may additionally comprise one or more unrelated sequences. In this context it will be understood that an “unrelated sequence” is a sequence which is not present in an SLRP (e.g. lumican, opticin or ketatocan) or infectious microorganism protein sequence from which any of the polypeptide(s) in the fusion polypeptide may correspond or share sequence homology with. Such a sequence will generally be referred to herein, in the context of a fusion protein/polypeptide, as a “fusion partner”. A fusion partner may, for example, be selected to assist with the production of the polypeptide(s). Examples of such fusion partners include those capable of enhancing recombinant expression of polypeptide(s) and those capable of facilitating or assisting purification of the polypeptide(s) such as an affinity tag. Alternatively, or in addition, a fusion partner may be selected to increase solubility of the polypeptide(s), to increase the immunogenicity of the polypeptide(s), and/or to enable the polypeptide(s) to be targeted to a specific or desired intracellular compartment.

Methods for the preparation of fusion polypeptides are known in the art and are described, for example, in Ausubel, et al., (eds) (2000-2010), “Current Protocols in Molecular Biology”, John Wiley & Sons, Inc., New York (see Chapter 16: “Protein Expression”). Typically, a fusion polypeptide may be made by standard techniques such as chemical conjugation, peptide synthesis or recombinant means. A fusion polypeptide may include one or more linker(s), such as peptide linker(s), between component parts of the protein, such as between one or more component peptides, and/or between one or more fusion partners and/or component peptides. Such peptide linker(s) may be chosen to permit the component parts of the fusion polypeptide to maintain or attain appropriate secondary and tertiary structure.

Polypeptide Variants and Fragments

Polypeptides of the invention may be modified by, for example, the deletion, addition and/or substitution of amino acid(s) that have minimal influence on the immunogenicity, secondary structure and/or hydropathic nature of the polypeptide. In general, the modifications do not substantially compromise the ability of the polypeptide to bind to a given MHC molecule.

Suitable amino acid substitutions include, but are not necessarily limited to, amino acid substitutions known in the art as “conservative”. A “conservative” substitution is one in which an amino acid is substituted for another amino acid that has similar properties, such that one skilled in the art of peptide chemistry would expect the biological activity, secondary structure and/or hydropathic nature of the polypeptide to be substantially unchanged. Amino acid substitutions may generally be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphipathic nature of the residues. For example, negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine and valine; glycine and alanine; asparagine and glutamine; and serine, threonine, phenylalanine and tyrosine. Other groups of amino acids that may represent conservative changes include: (1) ala, pro, gly, glu, asp, gin, asn, ser, thr; (2) cys, ser, tyr, thr, (3) val, ile, leu, met, ala, phe; (4) lys, arg, his; and (5) phe, tyr, trp, his. A modified polypeptide of the invention may also, or alternatively, contain non-conservative amino acid changes.

In certain embodiments, a polypeptide of the invention modified by the deletion, addition and/or substitution of amino acid(s) differs from the unmodified sequence by substitution, deletion or addition of five amino acids or fewer, such as by four, or three, or two, or one amino acid(s).

Included within the scope of the invention are variants of polypeptides of the invention. As used herein a polypeptide “variant” refers to a polypeptide with a substantially similar sequence. In general, two sequences are “substantially similar” if the two sequences have a specified percentage of amino acid residues that are the same (percentage of “sequence identity”). Accordingly, a “variant” of a polypeptide sequence of the invention may share at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 83% 85%, 88%, 90%, 93%, 95%, 96%, 97%, 98% or 99% sequence identity with the reference sequence.

In general, polypeptide sequence variants possess qualitative biological activity in common. Also included within the meaning of the term “variant” are homologues of polypeptides of the invention. A polypeptide homologue is typically from a different species but sharing substantially the same biological function or activity as the corresponding polypeptide disclosed herein. For example, homologues of polypeptides of the invention include, but are not limited to, those from different species of mammals or microorganisms.

Further, the term “variant” also includes analogues of polypeptides of the invention. A polypeptide “analogue” is a polypeptide which is a derivative of a given polypeptide, which derivative comprises addition, deletion, substitution of one or more amino acids, such that the polypeptide retains substantially the same function. As noted above, the term “conservative amino acid substitution” refers to a substitution or replacement of one amino acid for another amino acid with similar properties within a polypeptide chain (primary sequence of a protein).

In certain embodiments, a “variant” of a polypeptide of the invention differs in sequence (from the related polypeptide of the invention) by substitution, deletion or addition of five amino acids or fewer, such as by four, or three, or two, or one amino acid(s).

Also included within the scope of the invention are fragments of polypeptides of the invention. A polypeptide “fragment” is a polypeptide that encodes a constituent or is a constituent of a polypeptide of the invention or a variant thereof. Typically the fragment possesses qualitative biological activity in common with the polypeptide of which it is a constituent. Typically, the polypeptide fragment may be greater than 50 amino acids in length, between about 5 and about 50 amino acid residues in length, between about 5 and about 45 amino acid residues in length, between about 5 and about 40 amino acid residues in length, between about 5 and about 35 amino acid residues in length, between about 5 and about 30 amino acid residues in length, between about 5 and about 25 amino acid residues in length, between about 5 and about 20 amino acid residues in length, between about 5 and about 15 amino acid residues in length, or between about 5 and about 10 amino acid residues in length. In certain embodiments, a fragment of a polypeptide of the invention is 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more than 25 amino acid residues in length.

Exemplary Polypeptide Sequences

In certain embodiments, polypeptides of the invention comprise a sequence of at least six amino acid residues.

The sequence may share homology with a polypeptide from an infectious microorganism and a polypeptide of a human lumican polypeptide defined by residues 222-275 of the sequence set forth in SEQ ID NO: 1, or a fragment thereof. The sequence may share at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% sequence homology with a polypeptide of a human lumican polypeptide defined by residues 222-275 of the sequence set forth in SEQ ID NO: 1, or a fragment thereof.

The sequence may share homology with a polypeptide from an infectious microorganism and a polypeptide of a human lumican polypeptide defined by residues 222-247 of the sequence set forth in SEQ ID NO: 1, or a fragment thereof. The sequence may share at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% sequence homology with a polypeptide of a human lumican polypeptide defined by residues 222-247 of the sequence set forth in SEQ ID NO: 1, or a fragment thereof.

The sequence may share homology with a polypeptide from an infectious microorganism and a polypeptide of a human lumican polypeptide defined by residues 222-241 of the sequence set forth in SEQ ID NO: 1, or a fragment thereof. The sequence may share at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% sequence homology with a polypeptide of a human lumican polypeptide defined by residues 222-241 of the sequence set forth in SEQ ID NO: 1, or a fragment thereof.

The sequence may share homology with a polypeptide from an infectious microorganism and a polypeptide of a human opticin polypeptide defined by residues 264-315 of the sequence set forth in SEQ ID NO: 30, or a fragment thereof. The sequence may share at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% sequence homology with a polypeptide of a human opticin polypeptide defined by residues 264-315 of the sequence set forth in SEQ ID NO: 30, or a fragment thereof.

The sequence may share homology with a polypeptide from an infectious microorganism and a polypeptide of a human keratocan polypeptide defined by residues 71-91 of the sequence set forth in SEQ ID NO: 32, or a fragment thereof. The sequence may share at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% sequence homology with a polypeptide of a human keratocan polypeptide defined by residues 71-91 of the sequence set forth in SEQ ID NO: 32, or a fragment thereof.

The polypeptide from an infectious microorganism may comprise the amino acid sequence set forth in any one of SEQ ID NOs: 5-8, SEQ ID NOs: 36-38, or a fragment thereof. The sequence may share at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% sequence homology with a polypeptide from an infectious microorganism comprising the amino acid sequence set forth in any one of SEQ ID NOs: 5-8, SEQ ID NOs: 36-38, or a fragment thereof.

The polypeptide may comprise or consist of the amino acid sequence set forth in SEQ ID NO: 2, or a fragment thereof. In certain embodiments, the eighth amino acid (tyrosine) of the sequence set forth in SEQ ID NO: 2 may be substituted with another amino acid. For example, the eighth amino acid (tyrosine) of the sequence set forth in SEQ ID NO: 2 may be substituted with cysteine (SEQ ID NO: 3) or leucine (SEQ ID NO: 4).

The polypeptide may comprise or consist of the amino acid sequence set forth in SEQ ID NO: 34, or a fragment thereof. In certain embodiments, the third amino acid (tyrosine) of the sequence set forth in SEQ ID NO: 34 may be substituted with another amino acid. For example, the third amino acid (tyrosine) of the sequence set forth in SEQ ID NO: 34 may be substituted with cysteine (SEQ ID NO: 39) or leucine (SEQ ID NO: 40).

Certain embodiments of the invention relate to polypeptides comprising one or more fragments of the sequence set forth in SEQ ID NO: 1. A fragment of SEQ ID NO: 1 may comprise, for example, a constituent of SEQ ID NO: 1 comprising residues 224-232, 224-234, 226-234, 227-234, 229-235, 231-241, 236-244, or 235-243.

Certain embodiments of the invention relate to polypeptides comprising one or more fragments or variants of the sequence set forth in SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, or 34. The fragment or variant may comprise or consist of the sequence set forth in any one of SEQ ID NOs: 9-29 or SEQ ID NOs: 39-40.

Certain embodiments of the invention relate to polypeptides comprising or consisting of the amino acid sequence set forth in SEQ ID NO: 31, SEQ ID NO: 35, or a fragment thereof.

Certain embodiments of the invention relate to polypeptides comprising or consisting the amino acid sequence set forth in SEQ ID NO: 33, or a fragment thereof.

Polynucleotides

Also included within the scope of the invention are polynucleotides encoding polypeptides of the invention, and polynucleotides encoding variants and fragments of polypeptides of the invention.

As will be recognized by the skilled artisan, polynucleotides of the invention may be single-stranded (coding or antisense) or double-stranded, and may be DNA (genomic, cDNA or synthetic) or RNA molecules. RNA molecules include HnRNA molecules, which contain introns and correspond to a DNA molecule in a one-to-one manner, and mRNA molecules, which do not contain introns. Additional coding or non-coding sequences may, but need not, be present within a polynucleotide of the invention, and a polynucleotide may, but need not, be linked to other molecules and/or support materials. Polynucleotides may comprise a native sequence (i.e. an endogenous sequence that encodes a protein (e.g. an SLRP such as lumican, opticin or keratocan), a protein of an infectious microorganism, or a fragment thereof) or may comprise a variant, or a biological or antigenic functional equivalent of such a sequence. Polynucleotide variants may contain one or more substitutions, additions, deletions and/or insertions, as further described below, preferably such that the immunogenicity of the encoded polypeptide is not diminished, relative to a native HSV protein. The effect on the immunogenicity of the encoded polypeptide may generally be assessed as described herein. The term “variants” also encompasses homologous genes of xenogenic origin.

RNA may be derived from RNA polymerase-catalyzed transcription of a DNA sequence. The RNA may be a primary transcript derived from transcription of a corresponding DNA sequence. RNA may also undergo post-transcriptional processing. For example, a primary RNA transcript may undergo post-transcriptional processing to form a mature RNA. Messenger RNA (mRNA) refers to RNA derived from a corresponding open reading frame that may be translated into a protein by the cell. cDNA refers to a double-stranded DNA that is complementary to and derived from mRNA. Sense RNA refers to an RNA transcript that includes the mRNA and so can be translated into protein by the cell. Antisense RNA refers to an RNA transcript that is complementary to all or part of a target primary transcript of mRNA, and may be used to block the expression of a target gene.

The skilled addressee will recognise that RNA and cDNA sequences may be derived using the genetic code. An RNA sequence may be derived from a given DNA sequence by generating a sequence that is complementary to the particular DNA sequence. A complementary DNA (cDNA) sequence may be derived from a DNA sequence by deriving an RNA sequence from the DNA sequence as above, then converting the RNA sequence into a cDNA sequence.

In order to express a desired polypeptide or fusion polypeptide, the polynucleotide sequences encoding the polypeptide, fusion polypeptide, or functional equivalents, may be cloned into an appropriate vector (e.g. an expression a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence). The vector may comprise, for example, a DNA, RNA or complementary DNA (cDNA) sequence. The vector may be a plasmid vector, a viral vector, or any other suitable vehicle adapted for the insertion of foreign sequences, their introduction into cells and the expression of the introduced sequences. Typically the vector is an expression vector and may include expression control and processing sequences such as a promoter, an enhancer, ribosome binding sites, polyadenylation signals and/or transcription termination sequences. The invention also contemplates host cells transformed by such vectors. For example, polynucleotides encoding polypeptides of the invention may be cloned into a vector which is transformed into a bacterial host cell, (e.g. E. coli). Methods for the construction of vectors and their transformation into host cells are generally known in the art, and described in, for example, Sambrook et al., (1989), “Molecular Cloning: A Laboratory Manual”, 2nd ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.; and, Ausubel et al. (eds), (2000-2010), “Current Protocols in Molecular Biology”, John Wiley and Sons. Inc., New York.

The invention thus provides vectors (e.g. expression vectors) comprising polynucleotide sequence(s) of the invention. In some embodiments the vector may be an expression vector. The invention also provides methods for the preparation of a polypeptide of the invention, such a method comprising culturing a host cell comprising a polynucleotide or expression vector of the invention under conditions conductive to expression of the encoded polypeptide. In one embodiment, the method further comprises purifying the expressed polypeptide.

Preparation of Polypeptides, Fusion Polypeptides and Polynucleotides

Polypeptides of the invention or fusion proteins/polypeptides comprising polypeptide(s) of the invention may be manufactured using methods known in the art. For example, polypeptides of the invention may be manufactured by conventional methods used in peptide chemistry synthesis such as solid phase peptide synthesis, liquid phase peptide synthesis and recombinant gene technology. It will be understood that amino acid residues of polypeptides of the invention include any and all of their isomers (e.g. D-form, L-form and DL-form).

A polypeptide of the invention or a fusion polypeptide comprising a polypeptide of the invention as a component part thereof may be synthesised by solid phase chemistry techniques (see, for example, Steward et al., (1963), in “Solid Phase Peptide Synthesis”, H. Freeman Co., San Francisco; Meienhofer, (1973), in “Hormonal Proteins and Peptides”, volume 2, 46) or by classical solution synthesis (see, for example, Schroder et al. (1965), in “The Peptides”, volume 1, 72-75, Academic Press (New York). In general, such methods comprise the addition of one or more amino acids or suitably protected amino acids to a growing sequential polypeptide chain on a polymer. Typically, either the amino or carboxyl group of the first amino acid is protected by a suitable protecting group. The protected and/or derivatised amino acid is then either attached to an inert solid support or utilized in solution by adding the next amino acid in the sequence having the complimentary (amino or carboxyl) group suitably protected and under conditions suitable for forming the amide linkage. The protecting group may then be removed from the newly added amino acid residue and the next amino acid (suitably protected) is then added to form a growing polypeptide chain.

A polypeptide of the invention may be produced, for example, by digestion of a protein or larger polypeptide with one or more proteinases such as endoLys-C, endoArg-C, endoGlu-C and Staphylococcus V8-protease. The digested peptide fragments can be purified by, for example, high performance liquid chromatographic (HPLC) techniques.

Recombinant polypeptide production techniques will typically involve the cloning of a polynucleotide encoding a polypeptide of the invention into a plasmid for subsequent expression in a suitable microorganism. Suitable methods for the construction of expression vectors or plasmids are described in detail, for example, in standard texts such as Sambrook et al., (1989), “Molecular Cloning: A Laboratory Manual”, (2nd ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.; and, Ausubel et al. (eds), (2000-2010), “Current Protocols in Molecular Biology”, John Wiley and Sons, Inc., New York.

Recombinant methods suitable for producing a polypeptide of the invention or a fusion polypeptide comprising a polypeptide of the invention as a component part thereof are described in detail, for example, in standard texts such as Coligan et al., (eds) (2000-2010), “Current Protocols in Protein Science”, (Chapter 5), John Wiley and Sons, Inc.; and Pharmacia Biotech., (1994), “The Recombinant Protein Handbook”, Pharmacia Biotech.

Commonly used expression systems that may be used for the production of a polypeptide of the invention or a fusion polypeptide comprising the same include, for example, bacterial (e.g. E. coli), yeast (e.g. Saccharomyces cerevisiae, Aspergillus, Pichia pastorisis), viral (e.g. baculovirus and vaccinia), cellular (e.g. mammalian and insect) and cell-free systems. Suitable cell-free systems that may be used include, but are not limited to, eukaryotic rabbit reticulocyte, wheat germ extract systems, and the prokaryotic E. coli cell-free system (see, for example, Madin et al., Proc. Natl. Acad. Sci. U.S.A. 97:559-564 (2000), Pelham and Jackson, Eur. J. Hiochem., 67: 247-256 (1976); Roberts and Paterson, Proc. Natl. Acad. Sci., 70: 2330-2334 (1973); Zubay, Ann. Rev. Genet., 7: 267 (1973); Gold and Schweiger, Meth. Enzymol., 20: 537 (1971); Lesley et al., J. Biol. Chem., 266(4): 2632-2638 (1991); Baranov et al., Gene, 84: 463-466 (1989); and Kudlicki et al., Analyl. Biochem., 206: 389-393 (1992).

Changes to the amino acid sequence of a polypeptide of the invention or a fusion polypeptide comprising a polypeptide of the invention may be affected by standard techniques in the art. For example, amino acid changes may be affected by nucleotide replacement techniques which include the addition, deletion or substitution of nucleotides (conservative and/or non-conservative), under the proviso that the proper reading frame is maintained. Exemplary techniques include random mutagenesis, site-directed mutagenesis, oligonucleotide-mediated or polynucleotide-mediated mutagenesis, deletion of selected region(s) through the use of existing or engineered restriction enzyme sites, and the polymerase chain reaction. Testing the activity of modified polypeptides for the purposes of the invention may be via any one of a number of techniques known to those of skill in the art.

Purification of polypeptides of the invention or a fusion polypeptide comprising the same may be achieved using standard techniques in the art such as those described in Coligan et al., (eds) (2000-2010), “Current Protocols in Protein Science”, (Chapter 6), John Wiley and Sons, Inc., New York. For example, if the polypeptide is in a soluble state it may be isolated using standard methods such as column chromatography. Polypeptides of the invention may be genetically engineered to contain various affinity tags or carrier proteins that aid purification. For example, the use of histidine and protein tags engineered into an expression vector containing a polynucleotide encoding a polypeptide of the invention may facilitate purification by, for example, metal-chelate chromatography (MCAC) under either native or denaturing conditions. Purification may be scaled-up for large-scale production purposes.

A polypeptide of the invention, or a fusion polypeptide comprising a polypeptide of the invention as a component part thereof may be a soluble polypeptide or soluble fusion polypeptide.

Typically, a polypeptide of the invention is an isolated polypeptide. It will be understood that the term “isolated” in this context means that the polypeptide has been removed from or is not associated with some or all of the other components with which it would be found in its natural state. For example, an “isolated” polypeptide may be removed from other amino acid sequences within a larger polypeptide sequence, or may be removed from natural components such as unrelated proteins. For the sake of clarity, an “isolated” polypeptide also includes a polypeptide which has not been taken from nature but rather has been prepared de novo, such as for example by chemically synthesis and/or by recombinant methods. As described herein an isolated polypeptide of the invention may be included as a component part of a longer polypeptide or fusion polypeptide.

Polynucleotides encoding polypeptides of the invention can be manufactured using standard techniques known in the art such as those described, for example, in Sambrook et al. (1989) “Molecular Cloning: A Laboratory Manual”, (2nd ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.; Itakura K. et al. (1984), “Synthesis and use of synthetic oligonucleotides”, Annu. Rev. Biochem. 53:323; Innis et al., (eds), (1990), “PCR Protocols: A Guide to Methods and Applications”, Academic Press, New York; Innis and Gelfand, (eds), (1995), “PCR Strategies”, Academic Press, New York; and Innis and Gelfand, (eds), (1999), “PCR Methods Manual”, Academic Press, New York.

Polynucleotides encoding polypeptides of the invention may be manufactured, for example, by chemical synthesis techniques including the phosphodiester and phosphotriester methods (see, for example, Narang et al., (1979), “Improved phosphotriesler method for the synthesis of gene fragments”, Meth. Enzymol. 68:90; Brown et al. (1979), “Chemical Synthesis and Cloning of a Tyrosine IRNA Gene”, Meth. Enzymol. 68:109-151; and U.S. Pat. No. 4,356,270) or the diethylphosphoramidite method (see Beaucage and Caruthers, (1981), “Deoxynucleotide phosphoramidite”, Tetrahedron Letters, 22:1859-1862). A method for synthesising oligonucleotides on a modified solid support is described in U.S. Pat. No. 4,458,066.

Typically, a polynucleotide of the invention is an isolated polynucleotide. It will be understood that the term “isolated” in this context means that the polynucleotide has been removed from or is not associated with some or all of the other components with which it would be found in its natural state. For example, an “isolated” polynucleotide may be removed from other nucleic acid sequences within a larger nucleic acid sequence, or may be removed from natural components such as unrelated nucleic acids. For the sake of clarity, an “isolated” polynucleotide also includes a polynucleotide which has not been taken from nature but rather has been prepared de novo, such as chemically synthesised and/or prepared by recombinant methods.

Polypeptides of the invention may be modified with lipids, carbohydrates and/or phosphate groups to improve immunogenicity, stability and/or solubility. Capping of polypeptide termini may be used to enhance stability against cellular proteases. Polypeptides of the invention may be modified to induce apoptosis upon interaction with cells using methods known by those of skill in the art.

Antibodies

The invention provides antibodies “binding specifically” to one or more polypeptides of the invention and/or one or more fusion polypeptides of the invention (i.e. antibodies “specific for” one or more polypeptides/fusion polypeptides of the invention). By “binding specifically” or “specific for” it will be understood that the antibody is capable of binding to a target polypeptide of the invention with a significantly higher affinity than it binds to an unrelated molecule (e.g. a non-target polypeptide). Accordingly, an antibody that binds specifically to a polypeptide of the invention is an antibody with the capacity to discriminate between that polypeptide and any other number of potential alternative binding partners. Accordingly, when exposed to a plurality of different but equally accessible molecules as potential binding partners, an antibody specific for a target polypeptide of the invention will selectively bind to the target polypeptide and other alternative potential binding partners will remain substantially unbound by the antibody. In general, an antibody specific for a target polypeptide of the invention will preferentially bind to the target polypeptide at least 10-fold, preferably 50-fold, more preferably 100-fold, and most preferably greater than 100-fold more frequently than other potential binding partners that are not target polypeptides. An antibody specific for a polypeptide of the invention may be capable of binding to other non-target molecules at a weak, yet detectable level. This is commonly known as background binding and is readily discernible from target polypeptide-specific binding, for example, by use of an appropriate control.

Reaction conditions (e.g. concentration of antibody, incubation time, pH, temperature etc) to facilitate binding of antibodies to polypeptides of the invention will depend primarily on the antibody utilised and the specific target polypeptide, and may be readily determined using methods known in the art (see, for example, Ausubel et al., (eds), (2000-2010), “Current Protocols in Molecular Biology”, Vol. 1, John Wiley & Sons, Inc., New York; Coligan et al., (eds), (2000-2010), “Current protocols in Immunology”, John Wiley and Sons, Inc.; and Bonifacino et al., (eds) (2000-2010), “Current protocols in Cell Biology”, John Wiley and Sons, Inc.).

Antibodies capable of binding specifically to a polypeptide of the invention can be generated using methods known in the art.

For example, a monoclonal antibody specific for a target polypeptide of interest, typically containing Fab portions, may be prepared using the hybridoma technology described in Harlow and Lane (eds), (1988), “Antibodies—A Laboratory Manual”, Cold Spring Harbor Laboratory, N.Y.

In essence, in the preparation of monoclonal antibodies directed toward a target polypeptide, any technique that provides for the production of antibodies by continuous cell lines in culture may be used. These include the hybridoma technique originally developed by Kohler et al., (1975), “Continuous cultures of fused cells secreting antibody of predefined specificity”, Nature, 256:495-497, as well as the trioma technique, the human B-cell hybridoma technique (see Kozbor et al., (1983), “The Production of Monoclonal Antibodies From Human Lymphocytes”, Immunology Today, 4:72-79), and the EBV-hybridoma technique to produce human monoclonal antibodies (see Cole et al., (1985), in “Monoclonal Antibodies and Cancer Therapy”, 77-96, Alan R. Liss, Inc.). Immortal, antibody-producing cell lines can be created by techniques other than fusion, such as direct transformation of B lymphocytes with oncogenic DNA, or transfection with Epstein-Barr virus (see, for example, Schreier et al., (1980), “Hvbridoma Techniques”, Cold Spring Harbor Laboratory; Hammerling et al., (1981), “Monoclonal Antibodies and T-cell Hybridomas”, Elsevier/North-Holland Biochemical Press, Amsterdam; and Kennett et al., (1980), “Monoclonal Anibodies”, Plenum Press).

In summary, a means of producing a hybridoma from which the monoclonal antibody is produced, a myeloma or other self-perpetuating cell line is fused with lymphocytes obtained from the spleen of a mammal hyperimmunised with a recognition factor-binding portion thereof, or recognition factor, or an origin-specific DNA-binding portion thereof. Hybridomas producing a monoclonal antibody specific for a polypeptide of the invention are identified by their ability to immunoreact with the antigens present in that polypeptide.

A monoclonal antibody specific for a polypeptide of the invention can be produced by initiating a monoclonal hybridoma culture comprising a nutrient medium containing a hybridoma that secretes antibodies of the appropriate antigen specificity. The culture is maintained under conditions and for a time period sufficient for the hybridoma to secrete the antibody molecules into the medium. The antibody-containing medium is then collected. The antibody molecules can then be further isolated using known techniques.

Similarly, there are various procedures known in the art which may be used for the production of polyclonal antibodies. For the production of polyclonal antibodies specific for a polypeptide of the invention, various host animals can be immunized by injection with the polypeptide including, but not limited to, rabbits, chickens, mice, rats, sheep, goats, etc. Further, the polypeptide can be conjugated to an immunogenic carrier (e.g. bovine serum albumin (BSA) or keyhole limpet hemocyanin (KLH)). Also, various adjuvants may be used to increase the immunological response including, but not limited to, Freund's (complete and incomplete), mineral gels such as aluminium hydroxide, surface active substances such as rysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanins, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and Corynebacterium parvum.

Screening for the desired antibody can also be accomplished by a variety of techniques known in the art. Suitable assays for immunospecific binding of antibodies include, but are not limited to, radioimmunoassays, ELISAs (enzyme-linked immunosorbent assay), sandwich immunoassays, immunoradiometric assays, gel diffusion precipitation reactions, immunodiffusion assays, in situ immunoassays, Western blots, precipitation reactions, agglutination assays, complement fixation assays, immunofluorescence assays, protein A assays, immunoelectrophoresis assays, and the like (for description of such techniques see, for example, Ausubel et al., (eds), (2000-2010), “Current Protocols in Molecular Biology”, Vol. 1, John Wiley & Sons, Inc., New York). Antibody binding may be detected by virtue of a detectable label on the primary antibody. Alternatively, the antibody may be detected by virtue of its binding with a secondary antibody or reagent which is appropriately labelled. A variety of methods for detecting binding events in an immunoassay are known in the art, and are included in the scope of the invention.

In terms of obtaining a suitable amount of an antibody according to the invention, one may manufacture the antibodies using batch fermentation with serum free medium. After fermentation the antibody may be purified via a multistep procedure incorporating chromatography and viral inactivation/removal steps. For instance, the antibody may be first separated by Protein A affinity chromatography and then treated with solvent/detergent to inactivate any lipid enveloped viruses. Further purification, typically by anion and cation exchange chromatography, may be used to remove residual proteins, solvents/detergents and nucleic acids. The purified antibody may be further purified and formulated into 0.9% saline using gel filtration columns. The formulated bulk preparation may then be sterilised and viral filtered and dispensed.

Pharmaceutical Compositions

The invention provides pharmaceutical compositions comprising one or more polypeptide(s) of the invention and/or one or more fusion polypeptides/protein(s) comprising one or more polypeptide(s) of the invention. Accordingly, a pharmaceutical composition of the invention may comprise any one or more polypeptide(s) of the invention and/or any one or more polypeptide(s) of the invention as described above in the section above entitled “Polypeptides and Polynucleotides”.

Additionally or alternatively, a pharmaceutical composition of the invention may comprise an antibody specific for a polypeptide of the invention and/or an antibody specific for a fusion polypeptide of the invention (see subsectionabove entitled “Antibodies”).

Additionally or alternatively, a pharmaceutical composition of the invention may comprise a polynucleotide of the invention, a vector comprising a polynucleotide of the invention, and/or a host cell comprising a vector of the invention (see section above entitled “Polypeptides and Polynucleotides”).

A pharmaceutical composition of the invention may comprise a pharmaceutically acceptable carrier, adjuvant and/or diluent. The carriers, diluents and adjuvants must be “acceptable” in terms of being compatible with the other ingredients of the composition, and are generally not deleterious to the recipient thereof. Non-limiting examples of pharmaceutically acceptable carriers or diluents are demineralised or distilled water; saline solution; vegetable based oils such as peanut oil, safflower oil, olive oil, cottonseed oil, maize oil; sesame oils such as peanut oil, safflower oil, olive oil, cottonseed oil, maize oil, sesame oil, arachis oil or coconut oil; silicone oils, including polysiloxanes, such as methyl polysiloxane, phenyl polysiloxane and methylphenyl polysolpoxane; volatile silicones; mineral oils such as liquid paraffin, soft paraffin or squalane; cellulose derivatives such as methyl cellulose, ethyl cellulose, carboxymethylcellulose, sodium carboxymethylcellulose or hydroxypropylmethylcellulose; lower alkanols, for example ethanol or isopropanol; lower aralkanols; lower polyalkylene glycols or lower alkylene Jo glycols, for example polyethylene glycol, polypropylene glycol, ethylene glycol, propylene glycol, 1,3-butylene glycol or glycerin; fatty acid esters such as isopropyl palmitate, isopropyl myristate or ethyl oleate; polyvinylpyrolidone; agar; gum tragacanth or gum acacia, and petroleum jelly. Typically, the carrier or carriers will form from about 10% to about 99.9% by weight of the compositions.

Additionally or alternatively, a pharmaceutical composition of the invention may comprise an immunosuppressive agent, non-limiting examples of which include anti-inflammatory compounds, bronchodilatory compounds, cyclosporines, tacrolimus, sirolimus, mycophenolate mofetil, methotrexate, chromoglycalates, theophylline, leukotriene antagonist, and antihistamine, and combinations thereof. The immunosuppressive agent may also be an immunosuppressive drug or a specific antibody directed against B or T lymphocytes, or surface receptors that mediate their activation. For example, the immunosuppressive drug may be cyclosporine, tacrolimus, sirolimus, mycophenolate mofetil, methotrexate, chromoglycalates, theophylline, leukotriene antagonist, and antihistamine, or a combination thereof.

Additionally or alternatively, a pharmaceutical composition of the invention may comprise a steroid, such as a corticosteroid.

A pharmaceutical composition of the invention may be in a form suitable for administration by injection, in a form of a formulation suitable for oral ingestion (such as capsules, tablets, caplets, elixirs, for example), in a form of an ointment, cream or lotion suitable for topical administration, in a form suitable for delivery as an eye drop, in an aerosol form suitable for administration by inhalation, such as by intranasal inhalation or oral inhalation, or in a form suitable for parenteral administration, that is, subcutaneous, intramuscular or intravenous injection.

For administration as an injectable solution or suspension, non-toxic parenterally acceptable diluents or carriers can include, Ringer's solution, isotonic saline, phosphate buffered saline, ethanol and 1,2 propylene glycol.

Some examples of suitable carriers, diluents, excipients and adjuvants for oral use include peanut oil, liquid paraffin, sodium carboxymethylcellulose, methylcellulose, sodium alginate, gum acacia, gum tragacanth, dextrose, sucrose, sorbitol, mannitol, gelatine and lecithin. In addition these oral formulations may contain suitable flavouring and colourings agents. When used in capsule form the capsules may be coated with compounds such as glyceryl monostearate or glyceryl stearate which delay disintegration.

Adjuvants typically include emollients, emulsifiers, thickening agents, preservatives, bactericides and buffering agents.

Solid forms for oral administration may contain binders acceptable in human and veterinary pharmaceutical practice, sweeteners, disintegrating agents, diluents, flavourings, coating agents, preservatives, lubricants and/or time delay agents. Suitable binders include gum acacia, gelatine, corn starch, gum tragacanth, sodium alginate, carboxymethylcellulose or polyethylene glycol. Suitable sweeteners include sucrose, lactose, glucose, aspartame or saccharine. Suitable disintegrating agents include corn starch, methylcellulose, polyvinylpyrrolidone, guar gum, xanthan gum, bentonite, alginic acid or agar. Suitable diluents include lactose, sorbitol, mannitol, dextrose, kaolin, cellulose, calcium carbonate, calcium silicate or dicalcium phosphate. Suitable flavouring agents include peppermint oil, oil of wintergreen, cherry, orange or raspberry flavouring. Suitable coating agents include polymers or copolymers of acrylic acid and/or methacrylic acid and/or their esters, waxes, fatty alcohols, zein, shellac or gluten. Suitable preservatives include sodium benzoate, vitamin E, alpha-tocopherol, ascorbic acid, methyl paraben, propyl paraben or sodium bisulphite. Suitable lubricants include magnesium stearate, stearic acid, sodium oleate, sodium chloride or talc. Suitable time delay agents include glyceryl monostearate or glyceryl distearate.

Liquid forms for oral administration may contain, in addition to the above agents, a liquid carrier. Suitable liquid carriers include water, oils such as olive oil, peanut oil, sesame oil, sunflower oil, safflower oil, arachis oil, coconut oil, liquid paraffin, ethylene glycol, propylene glycol, polyethylene glycol, ethanol, propanol, isopropanol, glycerol, fatty alcohols, triglycerides or mixtures thereof.

Suspensions for oral administration may further comprise dispersing agents and/or suspending agents. Suitable suspending agents include sodium carboxymethylcellulose, methylcellulose, hydroxypropylmethyl-cellulose, poly-vinyl-pyrrolidone, sodium alginate or acetyl alcohol. Suitable dispersing agents include lecithin, polyoxyethylene esters of fatty acids such as stearic acid, polyoxyethylene sorbitol mono-or di-oleate, -stearate or -laurate, polyoxyethylene sorbitan mono-or di-oleate, -stearate or -laurate and the like.

The emulsions for oral administration may further comprise one or more emulsifying agents. Suitable emulsifying agents include dispersing agents as exemplified above or natural gums such as guar gum, gum acacia or gum tragacanth.

Methods for preparing parenterally administrable compositions are apparent to those skilled in the art, and are described in more detail in, for example, Remington's Pharmaceutical Science, 15th ed., Mack Publishing Company, Easton, Pa.

Topical formulations of the invention may comprise an active ingredient together with one or more acceptable carriers, and optionally any other therapeutic ingredients. Formulations suitable for topical administration include liquid or semi-liquid preparations suitable for penetration through the skin to the site where treatment is required, such as liniments, lotions, creams, ointments or pastes, and drops suitable for administration to the eye, ear or nose.

Drops according to the invention may comprise sterile aqueous or oily solutions or suspensions. These may be prepared by dissolving the active ingredient in an aqueous solution of a bactericidal and/or fungicidal agent and/or any other suitable preservative, and optionally including a surface active agent. The resulting solution may then be clarified by filtration, transferred to a suitable container and sterilised. Sterilisation may be achieved by autoclaving or maintaining at 90° C.-100° C. for half an hour, or by filtration, followed by transfer to a container by an aseptic technique. Examples of bactericidal and fungicidal agents suitable for inclusion in the drops are phenylmercuric nitrate or acetate (0.002%), benzalkonium chloride (0.01%) and chlorhexidine acetate (0.01%). Suitable solvents for the preparation of an oily solution include glycerol, diluted alcohol and propylene glycol.

Lotions according to the invention include those suitable for application to the skin or eye. An eye lotion may comprise a sterile aqueous solution optionally containing a bactericide and may be prepared by methods similar to those described above in relation to the preparation of drops. Lotions or liniments for application to the skin may also include an agent to hasten drying and to cool the skin, such as an alcohol or acetone, and/or a moisturiser such as glycerol, or oil such as castor oil or arachis oil.

Creams, ointments or pastes according to the invention are semi-solid formulations of the active ingredient for external application. They may be made by mixing the active ingredient in finely-divided or powdered form, alone or in solution or suspension in an aqueous or non-aqueous fluid, with a greasy or non-greasy basis. The basis may comprise hydrocarbons such as hard, soft or liquid paraffin, glycerol, beeswax, a metallic soap; a mucilage; an oil of natural origin such as almond, corn, arachis, castor or olive oil, wool fat or its derivatives, or a fatty acid such as stearic or oleic acid together with an alcohol such as propylene glycol or macrogols.

A pharmaceutical composition of the invention may incorporate any suitable surfactant such as an anionic, cationic or non-ionic surfactant such as sorbitan esters or polyoxyethylene derivatives thereof. Suspending agents such as natural gums, cellulose derivatives or inorganic materials such as silicaceous silicas, and other ingredients such as lanolin, may also be included.

A pharmaceutical composition of the invention may be administered in the form of a liposome. Liposomes are generally derived from phospholipids or other lipid substances, and are formed by mono-or multi-lamellar hydrated liquid crystals that are dispersed in an aqueous medium. Any non-toxic, physiologically acceptable and metabolisable lipid capable of forming liposomes can be used. The compositions in liposome form may contain stabilisers, preservatives, excipients and the like. The preferred lipids are the phospholipids and the phosphatidyl cholines (lecithins), both natural and synthetic. Methods to form liposomes are known in the art, and in relation to this specific reference is made to Prescott, (Ed), (1976), “Methods in Cell Biology”, Volume XIV, Academic Press, New York, N.Y. p. 33 et seq.

A pharmaceutical composition of the invention may be a vaccine. Polypeptide vaccines provide a number of advantages over other vaccine types including an absence of infectious materials that can compromise efficacy and/or trigger undesirable immune responses.

A vaccine of the invention may be administered to naïve recipients (i.e. individuals seronegative for particular infectious microorganism(s) associated with the onset of spondyloarthropathies), or primed recipients (i.e. individuals seropositive for particular infectious microorganism(s) associated with the onset of HLA-associated autoimmune diseases such as spondyloarthropathies and anterior uveitis).

A vaccine of the invention may be a preventative vaccine (i.e. a vaccine administered for the purpose of preventing HLA-associated autoimmune diseases) or a therapeutic vaccine (i.e. a vaccine administered for the purpose of treating HLA-associated autoimmune diseases). A vaccine of the invention may therefore be administered to a recipient for prophylactic, ameliorative, palliative, or therapeutic purposes.

Non-limiting examples of applicable HLA-associated autoimmune diseases include anterior uveitis (e.g. anterior acute uveitis) and spondyloarthropathies including ankylosing spondylitis, psoriatic arthritis, undifferentiated spondyloarthropathy, juvenile onset spondyloarthropathy, enteropathic arthritis, arthritis mutilans, reactive arthritis (Reiter's syndrome), reactive arthritides, sacroiliitis, spondylitis of inflammatory bowel disease, Crohn's disease associated with spondyloarthropathy, whipple disease, and Behcet disease.

A vaccine of the invention may be prepared according to standard methods known to those of ordinary skill in the art. Methods for vaccine preparation are generally described in Voller et al., (1978), “New Trends and Developments in Vaccines”, University Park Press, Baltimore, Md., USA.

A vaccine of the invention may comprise an adjuvant. The adjuvant will preferably enhance an immune response induced and/or enhance the specific vaccine, thereby improving protective efficacy. In certain embodiments the adjuvant will enable the induction of protective immunity utilising a lower dose of a polypeptide of the invention in the vaccine. A vaccine of the invention may comprise an adjuvant such as, for example, those described in the subsection above entitled “Pharmaceutical compositions”. A suitable adjuvant may be included in a vaccine of the invention in any suitable form (e.g. a powder, a solution, a non-vesicular solution, or a suspension).

Non-limiting examples of adjuvants suitable for inclusion in vaccines of the invention include those described in the section above entitled “Pharmaceutical compositions”. Further description regarding suitable adjuvants and methods for the preparation of vaccines are provided in “Vaccine Adjuvants: Preparation Methods and Research Protocols (Methods in Molecular Medicine)”, (2000), Ohagan (ed), Humana Press Inc.

Any suitable adjuvant may be included in a vaccine of the invention. For example, an aluminium-based adjuvant may be utilised. Suitable aluminium-based adjuvants include, but are not limited to, aluminium hydroxide, aluminium phosphate and combinations thereof. Other specific examples of aluminium-based adjuvants that may be utilised are described in European Patent No. 1216053 and U.S. Pat. No. 6,372,223. Additional non-limiting examples include polypeptide adjuvants such as interferons, interleukins, and other cytokines; AMPHIGEN, oil-in-water and water-in-oil emulsions; and saponins such as QuilA. Oil in water emulsions are well known in the art. In general, the oil in water composition will comprise a metabolizable oil, for example, a fish oil, a vegetable oil, or a synthetic oil. Examples of suitable oil in water emulsions include those described in European Patent No. 0399843, U.S. Pat. No. 7,029,678 and PCT publication No. WO 2007/006939. The oil in water emulsion may be utilised with other adjuvants and/or immunostimulants.

Other non-limiting examples of other suitable adjuvants include immunostimulants such as granulocyte-macrophage colony-stimulating factor (GM-CSF), monophosphoryl lipid A (MPL), cholera toxin (CT) or its constituent subunit, heat labile enterotoxin (LT) or its constituent subunit, toll like receptor ligand adjuvants such as lipopolysaccharide (LPS) and derivatives thereof (e.g. monophosphoryl lipid A and 3-Deacylated monophosphoryl lipid A), muramyl dipeptide (MDP), and F protein of Respiratory Syncytial Virus (RSV).

A vaccine of the present invention may be administered to a recipient in isolation or in combination with other additional therapeutic agent(s). In embodiments where the vaccine is administered with other additional therapeutic agent(s), the administration may be simultaneous, or may be sequential (i.e. vaccine administration followed by administration of the agent(s) or vice versa).

Prevention and Treatment of HLA-Associated Autoimmune Diseases

The invention provides methods for the prevention or treatment of an HLA-associated autoimmune disease comprising administering to a subject one or more polypeptides of the invention. The HLA-associated autoimmune disease may be an HLA-B27-associated autoimmune disease. In certain embodiments, the disease is a spondyloarthropathy or anterior uveitis.

Polypeptides of the invention may be administered to a subject in the form of a pharmaceutical composition of the invention (see section above entitled “Pharmaceutical compositions”). The pharmaceutical composition may be a preventative or therapeutic vaccine.

Preferably, the subject is a human. In certain embodiments, the human subject is positive for HLA-B27. The human subject may be homozygous or heterozygous for HLA-B27.

In alternative embodiments of the invention, the subject is a non-human mammal (e.g. a bovine, equine, ovine, non-human primate, or rodent species) and the autoimmune disease is an MHC-associated autoimmune disease. In certain embodiments, the disease is an MHC-associated spondyloarthropathy or anterior uveitis.

As discussed in detail above, polypeptides of the invention comprise region(s) of sequence homology with proteins derived from infectious microorganisms and SLRPs (e.g. lumican, opticin, keratocan) of host organisms susceptible to infection by those microorganisms. Without being restricted to particular mode(s) of action, it is proposed that administration of polypeptides of the invention to a subject may affect the immune response in several ways.

For example, administration of polypeptides of the invention to a subject may prime the immune system against infection by pathogenic microorganisms (e.g. bacteria and/or fungi) having protein(s) that share sequence homology with the administered polypeptides (i.e. induction of immunological memory). Priming of the host immune response may serve to prevent significant infection/re-infection of the host by said microorganisms. Preventing the chronic exposure of host immune cells (e.g. CD8⁺T lymphocytes) to antigenic determinants of infectious microorganisms sharing similarities with a host SLRP (e.g. lumican, opticin, keratocan) may assist in preventing the development of autoreactive immune cells that target and destroy cells and tissues expressing the SLRP.

Additionally or alternatively, administration of polypeptides of the invention to a subject may assist in re-inducing tolerance to antigenic determinants present in host SLRPs (e.g. lumican, opticin, keratocan). For example, administration of polypeptides of the invention comprising sequence motifs homologous to antigenic determinants of a host SLRP protein (e.g. lumican, opticin, keratocan) recognised by autoreactive immune cells and antibodies may induce tolerance to those determinants such that host SLRP is no longer recognised.

The methods of the invention may be used to prevent or treat an HLA-associated autoimmune disease. The HLA-associated autoimmune disease may be an HLA-B27-associated autoimmune disease. In certain embodiments, the disease is a spondyloarthropathy or anterior uveitis.

Non-limiting examples of spondyloarthropathies that may be treated and/or prevented using the methods of the invention include ankylosing spondylitis, psoriatic arthritis, undifferentiated spondyloarthropathy, juvenile onset spondyloarthropathy, enteropathic arthritis, arthritis mutilans, reactive arthritis (Reiter's syndrome), reactive arthritides, sacroiliitis, spondylitis of inflammatory bowel disease, Crohn's disease associated with spondyloarthropathy, whipple disease, and Behcet disease.

Non-limiting examples of anterior uveitis that may be treated and/or prevented using the methods of the invention include anterior acute uveitis and anterior chronic uveitis.

Although anterior uveitis and spondyloarthropathies such as those referred to above may be associated with the expression of HLA-B27 in humans, it will be understood that application of the methods provided herein are not limited to the prevention or treatment of autoimmune disease(s) in HLA-B27 positive subjects.

Accordingly, methods of the invention may be used for the prevention or treatment of MHC-associated autimmune disease(s) in subjects of any MHC subtype, including humans of any HLA subtype.

Administration to a subject of a polypeptide, composition or vaccine in accordance with the methods of the invention may be performed by any suitable route including, but not limited to, the parenteral (e.g. intravenous, intradermal, subcutaneous or intramuscular), mucosal (e.g. oral or intranasal) or topical route.

Accordingly, a polypeptide of the invention (or a composition/vaccine comprising the same) may be administered in a form suitable for administration by injection, in the form of a formulation suitable for oral ingestion (such as capsules, tablets, caplets, elixirs, for example), in the form of an ointment, cream or lotion suitable for topical administration, in a form suitable for delivery as an eye drop, in an aerosol form suitable for administration by inhalation, such as by intranasal inhalation or oral inhalation, or in a form suitable for parenteral administration, that is, subcutaneous, intramuscular or intravenous injection.

Formulations for intranasal administration may be provided in a freeze-dried powder form, in liquid form as nose drops, spray, or suitable for inhalation, as powder, as cream, or as emulsion.

In one embodiment, a polypeptide of the invention (or a composition/vaccine comprising the same) is provided in an oral form for administration to a subject in accordance with the methods of the invention. Oral administration may assist in methods of treatment designed to re-induce tolerance to antigen(s) present in self proteins sharing sequence homology with those of pathogenic bacterial protein(s).

In certain embodiments, polypeptides of the invention (or a composition/vaccine comprising the same) may be administered with a bio-scaffold.

A polypeptide of the invention (or a composition/vaccine comprising the same) used in the methods of the invention may be administered to a subject therapeutically or preventively.

In a therapeutic application, the polypeptide, composition or vaccine is administered to a subject already suffering from an HLA-associated autoimmune disease (e.g. a spondyloarthropathy or anterior uveitis) in an amount sufficient to cure or at least partially arrest the disease and its complications. Typically, in therapeutic applications, the treatment would be for the duration of the disease state or condition.

In a preventative application, the polypeptide, composition or vaccine is administered to a subject that is not suffering from an HLA-associated autoimmune disease (e.g. a spondyloarthropathy or anterior uveitis) at the time of administration. In particular, it is contemplated that administration of a vaccine of the invention to an individual previously exposed (i.e. primed) to a microorganism with antigenic determinants causative of spondyloarthropathies is beneficial in preventing the emergence of a spondyloarthropathy upon re-exposure of the subject to that microorganism.

The therapeutically effective dose level for any particular subject will depend upon a variety of factors including: the disease being treated and the severity/degree of progression of the disease; the subject's characteristics (e.g. age, body weight, general health, sex and diet of the subject); whether the compound is being used as single agent or combination therapy; the type of MHC restriction of the patient; the time of administration; the route of administration: the rate of sequestration of the polypeptide or composition (including vaccine); the duration of the treatment; the activity of the compound or agent employed; together with other related factors known in the art.

Various general considerations that may be considered when determining an appropriate dosage of a composition of the invention are described, for example, in Gennaro et al. (eds), (1990), “Remington's Pharmaceutical Sciences”, Mack Publishing Co., Easton, Pa., USA; and Gilman et al., (eds), (1990), “Goodman And Gilman's: The Pharmacological Bases of Therapeutics”, Pergamon Press.

Further, it will be apparent to one of ordinary skill in the art that the optimal quantity and spacing of individual dosages will be determined by the nature and extent of the spondyloarthropathy being treated, the form, route and site of administration, and the nature of the particular subject being treated.

One skilled in the art would be able, by routine experimentation, to determine an effective, non-toxic amount of a polypeptide, composition or vaccine of the invention which would be required to effectively prevent or treat an applicable spondyloarthropathy.

For example, an optimal dosage may be derived from administering serially diluted preparations comprising a polypeptide, composition or vaccine of the invention in conjunction with a suitable testing procedure. Additionally or alternatively, a matrix comprising various different dosages and dosage frequency can be designed and applied to one or more groups of experimental subjects to determine optimal dosages.

Generally, an effective dosage is expected to be in the range of about 0.0001 mg to about 1000 mg of active agent per kg body weight per 24 hours; typically, about 0.001 mg to about 750 mg of active agent of active agent per kg body weight per 24 hours; about 0.01 mg to about 500 mg of active agent per kg body weight per 24 hours; about 0.1 mg to about 500 mg of active agent per kg body weight per 24 hours; about 0.1 mg to about 250 mg of active agent per kg body weight per 24 hours; or about 1.0 mg to about 250 mg of active agent per kg body weight per 24 hours.

More typically, an effective dose range is expected to be in the range about 1.0 mg to about 200 mg of active agent per kg body weight per 24 hours; about 1.0 mg to about 100 mg of active agent per kg body weight per 24 hours; about 1.0 mg to about 50 mg of active agent per kg body weight per 24 hours; about 1.0 mg to about 25 mg of active agent per kg body weight per 24 hours; about 5.0 mg to about 50 mg of active agent per kg body weight per 24 hours; about 5.0 mg to about 20 mg of active agent per kg body weight per 24 hours; or about 5.0 mg to about 15 mg of active agent per kg body weight per 24 hours.

Alternatively, an effective dosage may be up to about 500 mg/m². Generally, an effective dosage is expected to be in the range of about 25 to about 500 mg/m, preferably about 25 to about 350 mg/m², more preferably about 25 to about 300 mg/m², still more preferably about 25 to about 250 mg/m², even more preferably about 50 to about 250 mg/m², and still even more preferably about 75 to about 150 mg/m².

In many instances, it will be desirable to have several or multiple administrations of a polypeptide of the invention (or a composition/vaccine comprising the same). For example, administration may occur 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more times. The administrations may be from about one to about twelve week intervals, and in certain embodiments from about one to about four week intervals. Periodic re-administration may be desirable in the case of recurrent exposure to a particular infectious microorganism targeted by a composition of the invention.

It will also be apparent to one of ordinary skill in the art that the optimal course of treatment can be ascertained using conventional course of treatment determination tests.

Where two or more therapeutic entities are administered to a subject “in conjunction”, they may be administered in a single composition at the same time, or in separate compositions at the same time or in separate compositions separated in time.

The efficacy of methods for preventing or treating diseases referred herein may be determined using standard techniques.

For therapeutic applications, such a determination will generally rely on establishing whether a given disease is cured or at least partially arrested in the treated subject.

For preventative applications, such a determination will generally rely on establishing whether the subject develops a given disease over a relevant time period following treatment, particularly upon re-exposure to microorganisms with antigenic determinants that are associated with spondyloarthropathies.

These factors may be established by clinical examination of the subject for symptoms and manifestations of the disease (e.g. a spondyloarthropathy or anterior uveitis) in question. Additionally or alternatively, diagnostic assays may be performed to detect the presence of absence of autoreactive immune cells and/or antibodies indicative of the disease (e.g. a spondyloarthropathy or anterior uveitis), or the likelihood of developing the disease in question. Non-limiting examples of such diagnostic assays are provided in the section below entitled “Diagnostic and prognostic assays”.

Medicaments

Polypeptides, fusion polypeptides/proteins, antibodies, polynucleotides, pharmaceutical compositions and/or vaccines of the invention may be used in the preparation of medicaments for treating or preventing HLA-associated autoimmune diseases. Also provided is use of a polypeptide, fusion polypeptide, antibody, polynucleotide, pharmaceutical composition and/or vaccine of the invention for treating an HLA-associated autoimmune disease.

The HLA-associated autoimmune disease may be an HLA-B27-associated autoimmune disease. In certain embodiments, the disease is a spondyloarthropathy or anterior uveitis.

Non-limiting examples of spondyloarthropathies that may be treated and/or prevented using polypeptides/proteins, antibodies, polynucleotides, pharmaceutical compositions, vaccines, and medicaments of the invention include ankylosing spondylitis, psoriatic arthritis, undifferentiated spondyloarthropathy, juvenile onset spondyloarthropathy, enteropathic arthritis, arthritis mutilans, reactive arthritis (Reiter's syndrome), reactive arthritides, sacroiliitis, spondylitis of inflammatory bowel disease, Crohn's disease associated with spondyloarthropathy, whipple disease, and Behcet disease.

Non-limiting examples of anterior uveitis that may be treated and/or prevented using using polypeptides/proteins, antibodies, polynucleotides, pharmaceutical compositions, vaccines, and medicaments of the invention include anterior acute uveitis and anterior chronic uveitis.

Diagnostic and Prognostic Assays

Polypeptides of the invention may be used in diagnostic and prognostic assays for HLA-associated autoimmune diseases. The HLA-associated autoimmune disease may be an HLA-B27-associated autoimmune disease. In certain embodiments, the disease is a spondyloarthropathy or anterior uveitis.

It has been determined that host immune cells and antibodies directed towards specific antigenic determinants in proteins of infectious microorganisms aberrantly recognise similar or identical antigenic determinants in host SLRPs (e.g. lumican, opticin or keratocan) instigating the destruction of cells and tissues in which those host proteins are expressed. The invention provides specific polypeptide sequences present in host SLRPs (e.g. lumican, opticin or keratocan) that are recognised by these autoreactive immune cells and antibodies, and hence a means of detecting the presence or absence of autoreactive immune cells and antibodies in a given subject.

The diagnostic and prognostic methods of the invention comprise detecting the presence or absence of an immune cell and/or protein specific for one or more polypeptides of the invention in a biological sample derived from a subject. The protein may be an antibody or an antibody fragment.

An immune cell and/or protein “specific for” a polypeptide of the invention will be capable of binding to the polypeptide with a significantly higher affinity than it binds to an unrelated molecule (e.g. another different polypeptide). Accordingly, an immune cell or protein (e.g. an antibody) that binds specifically to a polypeptide of the invention has the capacity to discriminate between that polypeptide and any other number of potential alternative binding partners. Accordingly, when exposed to a plurality of different but equally accessible molecules as potential binding partners, the immune cell or protein specific for a polypeptide of the invention will selectively bind to the polypeptide and other alternative potential binding partners will remain substantially unbound. In general, an immune cell or protein specific for a polypeptide of the invention will preferentially bind to the polypeptide at least 10-fold, preferably 50-fold, more preferably 100-fold, and most preferably greater than 100-fold more frequently than other potential binding partners. An immune cell or protein specific for a polypeptide of the invention may be capable of binding to other non-target molecules at a weak, yet detectable level. This is commonly known as background binding and is readily discernible from specific binding, for example, by use of an appropriate control.

The presence of an immune cell and/or protein specific for the polypeptide in a biological sample from the subject (i.e. “detecting the presence” of an immune cell and/or protein specific for the polypeptide) is indicative of a positive diagnosis for the HLA-associated autoimmune disease (e.g. an HLA-B27-associated autoimmune disease). In certain embodiments, the disease is a spondyloarthropathy or anterior uveitis.

Alternatively, failure to detect the presence of an immune cell and/or protein specific for the polypeptide in a biological sample from the subject (i.e. “detecting the absence” of an immune cell and/or protein specific for the polypeptide) is indicative of a negative diagnosis for the HLA-associated autoimmune disease (e.g. an HLA-B27-associated autoimmune disease). In certain embodiments, the disease is a spondyloarthropathy or anterior uveitis.

In certain embodiments, the presence of an immune cell and/or antibody specific for a polypeptide of the invention in the biological sample may be used for prognostic purposes. For example, the methods of the invention may be used to quantify the number or proportion of immune cells and/or antibodies specific for the polypeptide in a given biological sample which may be predictive of a particular disease state.

In other embodiments, the presence of an immune cell and/or antibody specific for the polypeptide in the biological sample may be indicative of a predisposition to developing an HLA-associated autoimmune disease in a subject (e.g. an HLA-B27-associated autoimmune disease). The disease may be a spondyloarthropathy or anterior uveitis. For example, the subject may be predisposed to developing the disease upon re-infection by an infectious microorganism that expresses a protein having sequence homology with the polypeptide.

Preferably, the subject is a human. In certain embodiments, the human subject is positive for HLA-B27. The human subject may be homozygous or heterozygous for HLA-B27.

In alternative embodiments of the invention, the subject is a non-human mammal (e.g. a bovine, equine, ovine, non-human primate, or rodent species) and the autoimmune disease is an MHC-associated autoimmune disease. In certain embodiments, the disease is an MHC-associated spondyloarthropathy or anterior uveitis.

The biological sample may be collected from an individual and used directly in the methods of the invention. Alternatively, the biological sample may be processed prior to use in the methods of the invention. For example, the biological sample may be purified, concentrated, separated into various components, or otherwise modified prior to use.

Non-limiting examples of biological samples include whole blood or a component thereof (e.g. plasma, serum), urine, saliva lymph, bile fluid, sputum, tears, cerebrospinal fluid, bronchioalveolar lavage fluid, synovial fluid, semen, ascitic tumour fluid, breast milk and pus.

It will be understood that a biological sample as contemplated herein includes cultured biological materials, including a sample derived from cultured cells, such as culture medium collected from cultured cells or a cell pellet. Accordingly, a biological sample may refer to a lysate, homogenate or extract prepared from a whole organism or a subset of its tissues, cells or component parts, or a fraction or portion thereof. A biological sample may also be modified prior to use, for example, by purification of one or more components, dilution, and/or centrifugation.

In certain embodiments, the diagnostic methods further comprise determining the MHC-type of the subject (e.g. the HLA-type of a human subject). Methods for HLA-typing are known in the art. Non-limiting examples of such methods include those described in U.S. Pat. No. 4,582,788, U.S. Pat. No. 4,683,202 and U.S. Pat. No. 5,545,526.

Diagnostic methods of the invention may be performed by contacting a biological sample from the subject with a polypeptide of the invention (e.g. one or more of those polypeptides referred to in the embodiments listed directly above) and detecting the presence or absence of an immune cell or protein of the biological sample specific for the polypeptide. A subject tested in accordance with the diagnostic methods may be a juvenile. A subject tested in accordance with the diagnostic methods may be a human juvenile positive for HLA-B27. A subject tested in accordance with the diagnostic methods may be an adult human positive for HLA-B27.

In certain embodiments, methods for determining a predisposition towards developing an HLA-associated autoimmune disease (e.g. a spondyloarthropathy or anterior uveitis) in a subject may be performed by contacting a biological sample from the subject with a polypeptide of the invention (e.g. one or more of those polypeptides referred to in the embodiments listed directly above) and detecting the presence or absence of an immune cell or protein of the biological sample specific for said polypeptide. A subject tested in accordance with the methods may be a juvenile. A subject tested in accordance with the methods may be a human juvenile positive for HLA-B27. A subject tested in accordance with the methods may be an adult human positive for HLA-B27. A subject tested in accordance with the methods will generally not be exhibiting symptoms of a spondyloarthropathy at the time of testing. However, in some circumstances the subject may be exhibiting mild symptoms of the spondyloarthropathy at the time of testing. In certain embodiments, the subject is a primed recipient (i.e. an individual seropositive for particular infectious microorganism(s) associated with the onset of spondyloarthropathies.

Non-limiting examples of immune cells of the sample specific for a polypeptide of the invention detectable by the methods include CD4⁺T lymphocytes, CD8⁺T lymphocytes and B lymphocytes.

Non-limiting examples of proteins of the sample specific for a polypeptide of the invention detectable by the methods include antibodies.

Reaction conditions (e.g. concentration of polypeptides, incubation time, pH, temperature etc) to facilitate binding of immune cells and proteins (e.g. antibodies) to polypeptides of the invention may be readily determined using methods known in the art (see, for example, Ausubel et al., (2000-2010), “Current Protocols in Molecular Biology”, Vol. 1, John Wiley & Sons, Inc., New York; Coligan et al. (eds), (2000-2010), “Current protocols in Immunology”, John Wiley and Sons, Inc.; and Bonifacino et al. (eds) (2000-2010), “Current protocols in Cell Biology”, John Wiley and Sons, Inc.).

In certain embodiments, the diagnostic methods involve detecting the binding of a polypeptide of the invention to an antibody present in a sample derived from a given subject. Accordingly, antibodies detectable by the methods are specific for a polypeptide of the invention. The antibody may be a human antibody. The human antibody may be of the isotype IgG (including IgG1, IgG2, IgG3 and IgG4 subisotypes), IgA (including IgA1 and IgA2 subisotypes), IgD, IgE, or IgM.

Antibodies specific for polypeptides of the invention may be detected using any method known in the art. Suitable examples of such methods include, but are not limited to, immunoblotting, enzyme-linked immunosorbent assay (ELISA), Western blotting, immunohistochemistry, immunocytochemistry, antibody-affinity chromatography, and variations/combinations thereof (see, for example, Coligan et al. (eds), (2000-2010), “Current protocols in Immunology”, John Wiley and Sons, Inc.).

For example, antibodies may be isolated and/or detected by immobilising a polypeptide (or a combination of polypeptides) of the invention onto a support, contacting the polypeptide immobilised on the support with a biological sample (e.g. purified peripheral blood mononuclear cells (PBMCs) or whole blood) under conditions suitable for binding to occur between antibodies within the sample and the immobilised polypeptide, then rinsing the support with a suitable reagent to remove unbound sample. The polypeptide may be immobilised on the support by direct binding or be bound indirectly to the support via one or more additional compounds. Non-limiting examples of suitable supports include assay plates (e.g. microtitre plates) or test tubes manufactured from polyethylene, polypropylene, polystyrene, sephadex, polyvinyl chloride, membranes (e.g. nitrocellulose membranes), beads/discs (including magnetic beads and discs) and particulate materials such as filter paper, nitrocellulose membrane, agarose, cross-linked dextran, and other polysaccharides.

In certain embodiments of the invention, the detection of an antibody bound to a polypeptide of the invention is performed using a detectable reagent capable of binding to the antibody. The reagent may bind to any region of the antibody including, but not limited to, the heavy chain, light chain, complementarity determining regions (CDRs), Fv, Fab or Fc regions. The reagent may be capable of binding to multiple regions of the antibody.

In one embodiment, the detectable reagent capable of binding to the antibody is a secondary antibody or an antigen-binding fragment thereof. Preferably, the secondary antibody is specific for a human antibody isotype. The human antibody isotype may be IgG (including IgG1, IgG2, IgG3 and IgG4 subisotypes), IgA (including IgA1 and IgA2 subisotypes), IgD, IgE, or IgM.

The secondary antibody may be conjugated to a detectable label, such as a fluorophore, enzyme, chromogen, catalyst, or direct visual label. Suitable enzymes for use as detectable labels on antibodies as contemplated herein include, but are not limited to, alkaline phosphatase and horseradish peroxidase, and are also described, for example, in U.S. Pat. No. 4,849,338 and U.S. Pat. No. 4,843,000. The enzyme label may be used alone or in combination with additional enzyme(s) in solution.

Methods for the generation of suitable secondary antibodies will be readily apparent to those skilled in the art and are described under the section above entitled “Antibodies”.

The detection of antibodies bound to a polypeptide of the invention may be performed as an enzyme-linked immunosorbent assay (ELISA). In general, the assay involves the coating of a polypeptide of the invention (a “capture reagent”) onto a solid support, such as the wells of a microtitre plate or a column, manufactured from a material such as polyethylene, polypropylene, polystyrene etc.

The polypeptide may be linked to the surface of the support, for example, by a non-covalent or covalent interaction or a physical linkage. Specific examples of methods for attachment of the capture reagents to supports are described in U.S. Pat. No. 4,376,110. If a covalent linkage is used, the cross-linking agent may be utilised to attach the capture reagent to the support (e.g. glutaraldehyde, N-hydroxy-succinimide esters, bifunctional maleimides).

The support may be treated with a blocking agent (e.g. non-fat milk, bovine serum albumin, casein, egg albumin) to prevent unwanted binding of material to excess sites on the surface of the support.

The sample may be administered to the surface of the support following coating and blocking. In general, the sample is diluted to an appropriate level using a suitable buffer. The degree of sample dilution and selection of an appropriate buffer will depend on factors such as the sample under analysis and the type of support utilised in the assay. These can be determined without inventive effort by those of ordinary skill in the art.

Once applied to the support coated with a polypeptide of the invention, the sample is generally incubated under conditions suitable to maximize sensitivity of the assay and to minimize dissociation. The incubation may be performed at a generally constant temperature, ranging from about 0° C. to about 40° C., and preferably ranging from about 20° C. to about 30° C. The pH of the incubation mixture will generally be in the range of about 4 to about 10, preferably in the range of about 6 to about 9, and more preferably in the range of about 7 to about 8. Various buffers may be employed to achieve and maintain the target pH during the incubation, non-limiting examples of which include Tris-phosphate, Tris-HCl borate, phosphate, acetate and carbonate. The incubation time is generally associated with the temperature, and will in general be less than about 12 hours to avoid non-specific binding. Preferably, the incubation time is from about 0.5 hours to about 3 hours, and more preferably from about 0.5 hours to about 1.5 hours at room temperature.

Following incubation, the sample may be removed from the immobilised polypeptide on the support, for example, by washing/rinsing the support. The pH of a suitable washing buffer will, in general, be in the range of about 6 to about 9 and preferably in the range of about 7 to about 8. The washing/rinsing may be done three or more times. The washing/rinsing may be performed using wash buffer generally at a temperatures from about 0° C. to about 40° C., and preferably from about 4° C. to about 30° C.

In a subsequent step, immobilised antibodies from the sample bound to polypeptides of the invention (on the support) are contacted with a detection reagent. Preferably, immobilised antibodies are contacted with a detection reagent at a temperature of about 20° C. to about 40° C., and preferably at a temperature of about 20° C. to about 25° C. In one embodiment, immobilised antibodies are contacted with a detection reagent at room temperature (RT) for about one hour. The detection reagent may be an antibody. In applications where the detectable reagent is an antibody, a molar excess of the antibody with respect to the maximum concentration of the molecules of the sample immobilised on the support is preferable. The antibody may be directly or indirectly detectable. The antibody may have a colorimetric label or a fluorometric label.

An additional antibody may be applied that binds to the detection reagent. The additional antibody may have a colorimetric label or a fluorometric label.

Determination of the presence and amount of an antibody bound to a polypeptide of in the invention can be achieved using methods known in the art, and will depend upon the detection reagent utilised. For example, detection may include colourimetry, chemiluminescence, or fluorometry. Detection and quantitative measurements may be conducted based on the signal derived from the detection reagent(s) compared to background signal derived from control samples. A standard curve may be generated to assist in determining the concentration of a polypeptide of the invention in a given sample.

In certain embodiments, the methods involve detecting the binding of a polypeptide of the invention to an immune cell present in a sample derived from a given subject.

Accordingly, immune cells detectable by the methods are specific for a polypeptide of the invention. In general, the immune cell will be specific for one or more antigenic determinants present in the polypeptide. Non-limiting examples of immune cells that may be specific for a polypeptide of the invention include CD4⁺T lymphocytes, CD8⁺T lymphocytes and B lymphocytes.

Immune cells specific for polypeptides of the invention may be detected using methods known in the art.

In general, the detection of antigen-specific T cells will require presentation of a polypeptide of the invention on MHC molecules. This may be achieved using tetramer-based assays. Alternatively, antigen-specific T cells in a given biological sample may be detected by exposing the sample to a polypeptide of the invention and measuring indicators of antigen-specific T cell activation (e.g. cell proliferation, cytokine secretion and/or cell surface expression of activation markers).

For example, a polypeptide of the invention or a combination of polypeptides of the invention may be mixed with a biological sample (e.g. purified peripheral blood mononuclear cells (PBMCs) or whole blood). The mixture may then be incubated for a suitable time period (e.g. 4-12 hours at 37° C.) facilitating the stimulation of immune cells that are specific for the polypeptide(s).

Immune cells specific for the polypeptide(s) may then be detected and/or enumerated using techniques known in the art. For example, the detection of immune cells specific for the polypeptide(s) may be performed by enzyme-linked immunosorbent assay (ELISA), analysing immune cell proliferation, analysing cytokine synthesis of immune cells, and/or analysing immune cell surface marker expression (such as by flow cytometry, ELISPOT, or other assays).

For example, immune cells specific for the polypeptide(s) may be detected and/or enumerated by measuring the expression of cellular activation markers (e.g. IFN-γ, IL-2, HLA-DR, CD25, CD69, CD38 and the like) by immune cells of the sample. In general, the detection of an upregulation in the expression of such activation markers in a subset of immune cells within the total cell population of the sample is indicative of the presence of immune cells specific for polypeptide(s) of the invention. Suitable controls (e.g. LPS stimulation) may be used to verify the integrity of such experiments.

The expression of cellular activation markers may be assessed by flow cytometry. The general principles of flow cytometry are known in the art, and assays for the preparation of cells for flow cytometry are described, for example, in Robinson et al., (eds), (2000-2010), “Current Protocols in Cytometry”, John Wiley and Sons, Inc.; Coligan et al., (eds) (2000-2010), “Current protocols in Immunology”, John Wiley and Sons, Inc.; U.S. Pat. No. 4,727,020, U.S. Pat. No. 4,704,891 and U.S. Pat. No. 4,599,307.

Additionally or alternatively, immune cells specific for polypeptide(s) of the invention may be detected by the identification and enumeration of cytokine-producing cells in the sample following stimulation. Suitable assays for achieving this purpose include ELISA-based assays (e.g. ELISPOTs).

Additionally or alternatively, immune cells specific for polypeptide(s) of the invention may be detected by measuring cell proliferation following stimulation of immune cells in the sample.

For example, the proliferation of immune cells specific for the polypeptide(s) may be assessed using a fluorescent dye assay. Fluorescent dye assays are well known in the art, and are described, for example in Parish C R. Immunol Cell Biol., (1999), 77(6):499-508; Lyons A B and Parish C R, Journal of Immunological Methods., (1994), 171:131-137; Horan et al., Methods in Cell Biology, (1990), 33:460-490; Lyons A B, J Immunol Methods, (2000), 21:243(1-2):147-54; Quah et al., Nat Protoc. (2007), 2(9):2049-56; Robinson et al. (2000-2010) (eds), “Current Protocols in Cytometry”, John Wiley and Sons, Inc., (see for example pp 9.11.1-9.11.9); Traycoff et al., Blood, (1995) 85:2059-2068; Young et al., Blood, (1996), 87; 545-556; Gothot et al., Experimental Hematology (1998), 26:562-570; Glimm and Eaves, Blood, (1999), 94:2161-2168, and Oostendorp et al., Blood, (2000), 95:855-862.

The skilled addressee will recognise that the methods for detecting and/or enumerating immune cells and proteins (e.g. antibodies) specific for polypeptide(s) of the invention described herein are non-limiting examples and other suitable methods known in the field may be utilised.

Kits

The invention provides kits for the diagnosis and prognosis of an HLA-associated autoimmune disease (e.g. an HLA-B27-associated autoimmune disease). In certain embodiments, the disease is a spondyloarthropathy or anterior uveitis. Kits of the invention may be fragmented kits. The kits comprise one or more polypeptides of the invention.

In certain embodiments, kits are provided for determining a predisposition towards developing an HLA-associated autoimmune disease (e.g. an HLA-B27-associated autoimmune disease). In certain embodiments, the disease is a spondyloarthropathy or anterior uveitis.

The kits may be used for the detection of an immune cell and/or protein specific for one or more polypeptide(s) of the invention in a biological sample. The protein may be an antibody or an antibody fragment. The immune cell may be a lymphocyte (e.g. a CD4⁺T lymphocyte, a CD8⁺T lymphocyte or a B lymphocyte).

Detection of the presence of an immune cell and/or protein in a sample specific for a polypeptide of the invention utilising a kit provided herein is indicative of a positive diagnosis for an HLA-associated autoimmune disease (e.g. an HLA-B27-associated autoimmune disease). In certain embodiments, the disease is a spondyloarthropathy or anterior uveitis.

Alternatively, failure to detect the presence of an immune cell and/or protein specific for a polypeptide of the invention utilising a kit provided herein is indicative of a negative diagnosis for an HLA-associated autoimmune disease (e.g. an HLA-B27-associated autoimmune disease). In certain embodiments, the disease is a spondyloarthropathy or anterior uveitis.

In certain embodiments, a kit of the invention may be used for prognostic purposes. For example, the kit may be used to quantify the number or proportion of immune cells and/or antibodies specific for a polypeptide of the invention in the sample of a subject which may be predictive of a particular disease state.

In other embodiments, the presence of an immune cell and/or antibody specific for the polypeptide in the sample may be indicative of a predisposition to developing an HLA-associated autoimmune disease in a subject (e.g. a spondyloarthropathy or anterior uveitis), for example, upon re-infection by an infectious microorganism containing a protein sharing sequence homology with a polypeptide of the invention.

A subject tested using a kit of the invention may be a human. In certain embodiments, the human subject is positive for HLA-B27. The human subject may be homozygous or heterozygous for HLA-B27. A subject tested using a kit of the invention may be a juvenile.

A subject tested using a kit of the invention may be a human juvenile positive for HLA-B27.

A subject tested using a kit of the invention may be an adult human positive for HLA-B27.

In alternative embodiments, a subject tested using a kit of the invention is a non-human mammal (e.g. a bovine, equine, ovine, non-human primate, or rodent species), and the kit is used for the diagnosis and/or prognosis of an MHC-associated autoimmune disease. In certain embodiments, the disease is an MHC-associated spondyloarthropathy or anterior uveitis.

The sample will generally be a biological sample. Non-limiting examples of biological samples include whole blood or a component thereof (e.g. plasma, serum), urine, saliva lymph, bile fluid, sputum, tears, cerebrospinal fluid, bronchioalveolar lavage fluid, synovial fluid, semen, ascitic tumour fluid, breast milk and pus.

It will be understood that a biological sample as contemplated herein includes cultured biological materials, including a sample derived from cultured cells, such as culture medium collected from cultured cells or a cell pellet. Accordingly, a biological sample may refer to a lysate, homogenate or extract prepared from a whole organism or a subset of its tissues, cells or component parts, or a fraction or portion thereof. A biological sample may also be modified prior to use, for example, by purification of one or more components, dilution, and/or centrifugation.

It will be understood that different combinations of polypeptides of the invention (e.g. two or more of those polypeptides referred to in the embodiments listed directly above) may included in kits of the invention.

In certain embodiments, a kit of the invention further comprises means for determining the MHC-type (e.g. HLA-type) of the subject.

Kits of the invention may include other components required to conduct the methods of the invention, such as antibodies, enzymes, buffers and/or diluents, MHC tetramers, reagents for flow cytometry and/or ELISAs/ELISPOT assays. The kits may comprise one or more means for obtaining a sample from a subject. The kits typically include containers for housing the various components and instructions for using the kit components in the methods of the invention.

Kits of the invention may comprise a suitable support on which one or more reagents are immobilised or may be immobilised. For example, kits of the invention may comprise a support coated with a polypeptide of the invention. Non-limiting examples of suitable supports include assay plates (e.g. microtitre plates) or test tubes manufactured from polyethylene, polypropylene, polystyrene, sephadex, polyvinyl chloride, plastic beads, and, as well as particulate materials such as filter paper, nitrocellulose membrane, agarose, cross-linked dextran, and other polysaccharides.

In certain embodiments, kits of the invention may be used to perform an enzyme-linked immunosorbent assay (ELISA) or an ELISPOT assay.

Additionally or alternatively, kits of the invention may be used to perform western blotting, analyse immune cell proliferation, analyse cytokine synthesis of immune cells, and/or analyse immune cell surface marker expression.

It will be appreciated by persons skilled in the art that numerous variations and/or modifications may be made to the invention as shown in the specific embodiments without departing from the spirit or scope of the invention as broadly described. The present embodiments are, therefore, to be considered in all respects as illustrative and not restrictive.

EXAMPLES

The invention will now be described with reference to specific examples, which should not be construed as in any way limiting.

Example 1 Identification of Autoreactive Lumican Peptide Sequences Materials and Methods (i) Proteomic Analyses

Aqueous humor from patients with anterior acute uveitis (AAU) was spun to dry pellet in a speedyvac and resuspended in CH₃CN to adjust to pH8. Sequencing grade porcine trypsin was added at 16 ng/μl to sample and placed in 37 degree oven overnight.

Tryptic digest peptides were separated by on-line cation exchange (SCX) and C18 IJ nano-LC using an Ultimate HPLC, Switchos and Famos autosampler system (LC-Packings, Amsterdam, Netherlands). Peptides (20 μl) were diluted in 20 μl 0.1% v/v formic acid followed by 20 μl of 100% CH3CN loaded onto a SCX microtrap (168 mm; Michrom Bioresources, Auburn, Calif., USA) at 20 l/min. Peptides were eluted using 10 pt volumes of ammonium acetate. The unbound load fraction and each salt step were concentrated and desalted using a micro C18 precolumn (500 μm×2 mm; Michrom Bioresources) with H₂O:CH₃CN (98:2, 0.1% formic acid) at 20 pd/min. After a 10 min wash the precolumn was switched (Switchos) into line with a fritless analytical C18 column (75 μm×12 cm) and peptides eluted using a linear gradient of H₂O:CH₃CN (95:5, 0.1% formic acid-buffer A) to H₂O:CH₄CN (40:60, 0.1% formic acid-buffer B) at 200 nl/min over 30 min.

Peptide digests were analysed using LC-MS/MS and was carried out using Thermo Finnigan's LTQ-FT/MS. Peptides were loaded on to a peptide trap cartridge (Agilent, Palo Alto, Calif.) at a flow rate of 1 μL/min. Trapped peptides were then eluted onto a reversed-phase PicoFrit column using a linear gradient of acetonitrile (0-60%) in 0.1% formic acid using a 250 nL/min flow rate. Eluted peptides from the PicoFrit column were sprayed into the LCQ Deca XP mass spectrometer equipped with a nano-spray ion source. Data-dependent acquisition mode was enabled, and each survey MS scan was followed by three MS/MS scans with dynamic exclusion option on. To reduce carry-over, each LC-MS run was followed by a blank injection of buffer and run with the same gradient. MS data were acquired in a repeating 4-s cycle. Dynamic exclusion was set to 1 min. The instrument calibration was performed using Calmix (caffeine, MRFA, and ultramark) according to manufacturer's instructions. The spray voltage was 2.1 kV for LCQ or 1.8 kV for LTQ-FT, while the temperature of ion transfer tube was set at 160° C. The normalized collision energy was set at 35%. FT-ICR survey scans were acquired at the resolution of 100 000 (m/z=400).

(ii) Database Search for Protein Identification

Processing scripts generated data suitable for submission to the database search program MASCOT (http://www.matrixscience.com) using the Homo sapiens taxonomies. Using Mascot, the data sets were searched against NCBI and SwissProt databases to help eliminate redundancies and identify proteins that might appear in only one database. The precursor ion mass tolerance was set at ±6 ppm, and trypsin was designated as the proteolytic enzyme with up to 1 missed cleavage.

(iii) Lumican Expression in Irus and Synovial Tissues

Human irus pigment epithelial cell (IPE), iris tissues, and synovial tissues were labelled with anti-lumican or control rabbit IgG, followed by HRP or Alexa-fluor conjugated goat anti-rabbit IgG.

(iv) HLA-Binding Affinity

The binding affinity of peptides to HLA-B27 was predicted using BIMAS (http://www.bimas.dcrt.nih.gov/molbio/hla_bind/), T cell epitope prediction models (see http://tools.immuneepitope.org/main/html/tcell_tools.html), and SYFPEITHI (http://www.syfpeithi.de/Scripts/MHCServer.dll/EpitopePrediction.htm).

The SYFPEITHI prediction is based on previous publications on T-cell epitopes and MHC ligands, a scoring system that evaluates every amino acid within a given peptide (see, for example, Rammensee et al., (1995), “MHC ligands and peptide motifs: 1st listing, Immunogenetics” 41, 178-228; Rammensee et al. (1997), “MHC ligands and peptide motifs”, Landes Bioscience (International distributor—except North America: Springer Verlag GmbH & Co. KG, Tiergartenstr. 17, D-69121 Heidelberg; Brander and Walker, (1996), “The HLA-class I CTL response in HIV-1 infection: Identification of optimal epitopes”, Los Alamos, N. Mex.: Los Alamos National Laboratory, Theoretical Biology and Biophysics; and Stevanovic et al. (1995), “Oberflachenantigene im Nierenzellkarzinom—Präsentation von MHC I-gebundenen Selbstpeptiden”, Akt. Urol. Sonderheft (26): 45-46.

The prediction is based on published motifs (pool sequencing, natural ligands) and takes into consideration the amino acids in the anchor and auxiliary anchor positions, as well as other frequent amino acids. The score is calculated according to the following rules: The amino acids of a certain peptide are given a specific value depending on whether they are anchor, auxiliary anchor or preferred residue. Ideal anchors will be given 10 points, unusual anchors 6-8 points, auxiliary anchors 4-6 and preferred residues 1-4 points. Amino acids that are regarded as having a negative effect on the binding ability are given values between −1 and −3.

Results

The proteomics investigation to generate an expression profile of the aqueous humor (AH) of anterior acute uveitis (AAU) subjects using mass spectrometry identified similar expression sequences between lumican and the outer membrane glycoprotein (OMP) of Chlamylia. It was determined that regions of the human lumican sequence share strong sequence homology with the Chlamydia OMP.

As shown in FIG. 1, lumican is expressed in tissues associated with both spondyloarthropies and uveitis. For example, lumican was found to be expressed in human iris epithelial cell (IPE) cultures (FIGS. 1A and 1E), iris tissues (FIGS. 1B and 1F), and synovial tissues (FIGS. 1C, 1D, 1G and 1H). Lumican staining is present in IPE in vitro (FIG. 1E) and in vivo (FIG. 1F), in blood vessels (bv) (FIG. 1G) and in articular cartilage (FIG. 1H).

On that basis it was proposed that the immune system mal-recognises specific sequences in lumican as foreign in Chlamydia-exposed individuals leading to spondyloarthropathies. It is postulated that this effect may arise from molecular mimicry whereby a similarity exists between antigen(s) of host protein and those of a pathogen protein (e.g. similar structure either in amino acid sequence or conformational-fit) despite the proteins originating from dissimilar genes. Exposure to the foreign antigen of the pathogen can elicit a cross-reactive immune response against both the foreign antigen and the similar self-molecule. Subsequently, an infection by the pathogen can trigger a chronic autoimmune reaction and further chronic exposure will eventually initiate the destruction of tissues.

Given that some individuals not previously exposed to Chlamydia still develop spondyloarthropathies, it was also postulated that spondyloarthropathies may not be linked exclusively with Chlamydia infection. In such cases, spondyloarthropathies may arise by a similar mechanism upon exposure other bacteria and their proteins and it was subsequently identified that a protein of Aspergillus nidulans comprises a peptide sequence with strong sequence homology to lumican. This is proposed to account (at least in part) for the observation that individuals not previously exposed to Chlamydia can still develop spondyloarthropathies.

The degree of sequence homology shared between a region of the human lumican protein and bacterial and fungal protein sequences and is shown in Table 1 below.

TABLE 1 homology of bacterial and final protein sequences with human lumican sequences Sequence Bacterial Protein Human lumican Sequence Homology Chlamydia trachomatis DEYFKRFNALQYLRLSHNELADSGIP 77% fructose biphosphate aldolase (GenBank # P51884: residues 222-247) protein (GenBank # Q3KL49) Chlamydia trachomatis DEYFKRFNALQYLRLSHNEL 44% OMP85 protein (GenBank # P51884: residues 222-241) (GenBank # Q3KMCI) Chlamydia trachomatis DEYFKRFNALQYLRLSHNEL 71% serine protease do-like (GenBank # P51884: residues 222-241) (Swiss-Prot # P18584.2) Aspergillus nidulans YFKRFNALQYL 81% uncharacterised protein (GenBank # P51884: residues 224-234) (GenBank # Q5AR12)

Using BIMAS the peptide sequence the lumican peptide sequence identified was predicted to possess strong binding affinity to HLA-B27.

The lumican peptide sequence identified was also analysed using SYFPEITHI. Strong binding affinity is claimed as a score higher than 15, and the peptide obtained a score of 28 as indicated in Table 2.

TABLE 2 HLA-B27 binding prediction scores for human ocular lumican peptide using SYFPEITHI and BIMAS Score Score Human sequence (SYFPEITH) (BIMAS) DEYFKRFNALQYLRLSHNELADSGIP 28 30000 (GenBank # P51884: residues 222-247)

The SYFPEITHI scoring system evaluates every amino acid within a given peptide. Individual amino acids may be given the arbitrary value 1 for amino acids that are only slightly preferred in the respective position, optimal anchor residues are given the value 15: any value between these two is possible. The allocation of values is based on the frequency of the respective amino acid in natural ligands, T-cell epitopes, or binding peptides. To ensure that the results were not biased, the entire human lumican sequence as displayed in Table 3 (GenBank #P51884) was blasted against microbial sequences using the swissprot database (see http://www.expasy.org/tools/blast/).

Furthermore, the entire sequence was processed using T cell epitope prediction models (see http:/tools.immuneepitope.org/main/html/tcell_tools.html). These tools predict the IC50 values for peptides binding to specific MHC molecules, as shown in Table 4 where the lowest amount of concentration represents the lowest amount of molecule required to elicit a T-cell response. The highest and lowest scores obtained using this software were an exact match to the sequence homology of lumican to the Aspergillus nidulans protein displayed in Table 1. This ensures that the sequence is bound by HLA-B27 with high affinity (Table 4, IC50 of 93 nm) and thus induces an immune response when subjected to HLA-B27 T cells. Moreover, it suggests that an HLA-B27 positive individual exposed to Chlamydia or Aspergillus produces an immune response that stimulates a T-cell selection and clonal expansion. Subsequent and chronic exposure will ensure an attack on the lumican protein since T-cells mal-recognized it as foreign. Accordingly, the Chlamydia-lumican and Aspergillus-lumican mimicry leads to the leading missing link and formation spondyloarthropathies such as ankylosing spondylitis, juvenile arthritis, psoriasis and uveitis.

TABLE 3 the full seq uence of human lumican (GenBank # P51884) 1 MSLSAFTLFL ALIGGTSGQY YDYDFPLSIY GQSSPNCAPE CNCPESYPSA MYCDELKLKS 61 VPMVPPGIKY LYLRNNQIDH IDEKAFENVT DLQWLILDHN LLENSKIKGR VFSKLKQLKK 121 LHINHNNLTE SVGPLPKSLE DLQLTHNKIT KLGSFEGLVN LTFIHLQHNR LKEDAVSAAF 181 KGLKSLEYLD LSFNQIARLP SGLPVSLLTL YLDNNKISNI PDEYFKRFNA LQYLRLSHNE 241 LADSGIPGNS FNVSSLVELD LSYNKLKNIP TVNENLENYY LEVNQLEKFD IKSFCKILGP 301 LSYSKIKHLR LDGNRISETS LPPDMYECLR VANEVTLN

TABLE 4 the combined predictors of proteasomal processing, TAP transport, MHC 1 binding to produce an overall score for each peptide's intrinsic potential of being a T cell epitope Proteosome TAP MHC Processing Total MHC IC50 Allele Position Pep Length Sequence Score Score Score Score Score nM HLA B*2705 1:2-10 9.0000 SLSAFTLFL 1.3800 0.4600 −4.4000 1.8400 −2.5600 24862.1000 HLA B*2705 1:131-139 9.0000 SVGPLPKSL 1.3700 0.3600 −5.2200 1.7200 −3.4900 164157.9000 HLA B*2705 1:301-309 9.0000 LSYSKIKHL 1.3500 0.4500 −4.4100 1.8000 −2.6000 25420.8000 HLA B*2705 1:202-210 9.0000 GLPVSLLTL 1.3400 0.3600 −4.6800 1.7000 −2.9800 47471.1000 HLA B*2705 1:63-71 9.0000 MVPPGIKYL 1.3000 0.4300 −5.4200 1.7300 −3.6900 265554.3000 HLA B*2705 1:14-22 9.0000 GGTSGQYYD 1.3000 −0.9900 −5.3700 0.3100 −5.0600 235429.6000 HLA B*2705 1:233-241 9.0000 YLRLSHNEL 1.3000 0.4200 −4.7900 1.7100 −3.0800 62221.3000 HLA B*2705 1:46-54 9.0000 SYPSAMYCD 1.2700 −0.7300 −5.8900 0.5400 −5.3500 774085.2000 HLA B*2705 1:166-174 9.0000 LQHNRLKED 1.2400 −0.7500 −4.4600 0.4900 −3.9800 29123.6000 HLA B*2705 1:251-259 9.0000 FNVSSLVEL 1.2300 0.3700 −4.5600 1.6000 −2.9600 36427.8000 HLA B*2705 1:250-258 9.0000 SFNVSSLVE 1.2200 −0.5600 −5.9700 0.6600 −5.3100 929644.7000 HLA B*2705 1:329-337 9.0000 LRVANEVTL 1.2200 0.5400 −2.8300 1.7600 −1.0700 682.7000 HLA B*2705 1:321-329 9.0000 LPPDMYECL 1.2200 0.3000 −5.8100 1.5200 −4.2900 646609.2000 HLA B*2705 1:228-236 9.0000 FNALQYLRL 1.2100 0.3700 −4.0200 1.5900 −2.4300 10510.6000 HLA B*2705 1:170-178 9.0000 RLKEDAVSA 1.2100 −0.0600 −4.1800 1.1500 −3.0300 15078.1000 HLA B*2705 1:226-234 9.0000 KRFNALQYL 1.2000 0.5600 −1.9700 1.7600 −0.2100 93.1000 HLA B*2705 1:65-73 9.0000 PFGIKYLYL 1.2000 0.0300 −6.0400 1.2200 −4.8200 1102999.8000

IC50 values were also predicted for binding of lumican nonamers commencing at positions 235 and 236 to various HLA-A and HLA-B alleles (Table 5).

TABLE 5 predicted IC50 values for binding of lumican nonamers to various HLA-A and HLA-B alleles Position of nonamer HLA in Lumican IC50 Allele polypeptide PepLength Sequence [nM] HLA 225-233 9 FKRFNALQY 1.2 B*1503 HLA 226-234 9 KRFNALQYL 93.1 B*2705 HLA 226-234 9 KRFNALQYL 143.4 B*1503 HLA 226-234 9 KRFNALQYL 163.7 A*0202 HLA 225-233 9 FKRFNALQY 265.4 A*8001 HLA 226-234 9 KRFNALQYL 404.1 A*3001 HLA 225-233 9 FKRFNALQY 508.5 A*2902 HLA 226-234 9 KRFNALQYL 1047.6 A*3201 HLA 225-233 9 FKRFNALQY 1415.3 A*3001 HLA 226-234 9 KRFNALQYL 1624.5 B*4002 HLA 225-233 9 FKRFNALQY 1818.9 A*3002 HLA 226-234 9 KRFNALQYL 2156.9 A*0203 HLA 226-234 9 KRFNALQYL 2158.6 A*0201 HLA 225-233 9 FKRFNALQY 2699.8 B*3501 HLA 226-234 9 KRFNALQYL 3903.0 B*4801 HLA 236-244 9 KRFNALQYL 4492.9 A*2301 HLA 236-244 9 KRFNALQYL 4652.1 A*2403 HLA 235-243 9 FKRFNALQY 5413.4 B*1501 HLA 236-244 9 KRFNALQYL 6168.3 B*0801

SYFPEITHI results (Tables 6-20) indicated that HLA-A and HLA-B alleles have a strong affinity for at least the following lumican nonamers and octamers (strong binding affinity is claimed as a score higher than 15).

TABLE 6 HLA-A*03 HLA-A*03 nonamers Predicted Position in lumican binding polypeptide 1 2 3 4 5 6 7 8 9 score 230 A L  Q Y L R L S H 23 225 F K  R F N A L Q Y 18

TABLE 7 HLA-A*2402 HLA-A*2402 nonamers Predicted Position in lumican binding polypeptide 1 2 3 4 5 6 7 8 9 score 213 E Y F K R F N A L 32

TABLE 8 HLA-B*08 HLA-B*08 nonamers Predicted Position in lumican binding polypeptide 1 2 3 4 5 6 7 8 9 score 233 Y L R L S H N E L 24

TABLE 9 HLA-B*1402 HLA-B*1402 nonamers Predicted Position in lumican binding polypeptide 1 2 3 4 5 6 7 8 9 score 226 K R F N A L Q Y L 25

TABLE 10 HLA-B*2705 HLA-B*2705 nonamers Position in lumican Predicted binding polypeptide 1 2 3 4 5 6 7 8 9 score 226 K R F N A L Q Y L 26

TABLE 11 HLA-B*2709 HLA-B*2709 nonamers Position in lumican Predicted polypeptide 1 2 3 4 5 6 7 8 9 binding score 226 K R F N A L Q Y L 24

TABLE 12 HLA-B*3901 HLA-B*3901 nonamers Position in lumican Predicted polypeptide 1 2 3 4 5 6 7 8 9 binding score 226 K R F N A L Q Y L 21

TABLE 13 HLA-B*3902 HLA-B*3902 nonamers Position in lumican Predicted polypeptide 1 2 3 4 5 6 7 8 9 binding score 226 K R F N A L Q Y L 16

TABLE 14 HLA-B*1402 (octamer) HLA-B*1402 octamers Position in lumican Predicted polypeptide 1 2 3 4 5 6 7 8 binding score 234 L R L S H N E L 25

TABLE 15 HLA-B*1402 (nonamer) HLA-B*1402 nonamers Position in lumican Predicted polypeptide 1 2 3 4 5 6 7 8 9 binding score 226 K R F N A L Q Y L 25

TABLE 16 HLA-B*3801 HLA-B*3801 nonamers Position in lumican Predicted polypeptide 1 2 3 4 5 6 7 8 9 binding score 226 K R F N A L Q Y L 17 225 F K R F N A L Q Y 0

TABLE 17 HLA-B*2709 HLA-B*2709 nonamers Position in lumican Predicted polypeptide 1 2 3 4 5 6 7 8 9 binding score 226 K R F N A L Q Y L 24

TABLE 18 HLA-A*26 HLA-A*26 nonamers Position in lumican Predicted polypeptide 1 2 3 4 5 6 7 8 9 binding score 226 K R F N A L Q Y L 16

TABLE 19 HLA-A*01 HLA-A*01 nonamers Position in lumican Predicted polypeptide 1 2 3 4 5 6 7 8 9 binding score 225 F K R F N A L Q Y 18

TABLE 20 H2-Kd H2-Kd nonamers Position in lumican Predicted polypeptide 1 2 3 4 5 6 7 8 9 binding score 226 K R F N A L Q Y L 15

Example 2 HLA B27 Peptide Binding Assay Materials and Methods

HLA B27 epitope analyses were conducted using The REVEAL & ProVE® Rapid Epitope Discovery System.

(i) Peptide Synthesis:

37×9-mer peptides from Lumican and Chlamydia trachomatis were synthesized (see Table 21). The peptides were synthesized as a Prospector PEPscreen®: Custom Peptide Library. Peptides were synthesized in 0.5-2 mg quantities with high average purity. Quality control by MALDI-TOF Mass Spectrometry was carried out all of samples.

TABLE 21 Custom peptides were generated using Prospector PEPscreen ® custom peptide library synthesis. I.D. Peptide 1 KRFNALQYL 2 RRQLEDIRL 3 LRLSHNELA 4 LQYLRLSHN 5 EHKHTRRQL 6 HKHTRRQLE 7 KHTRRQLED 8 HTRRQLEDI 9 TRRQLEDIR 10 RRQLEDIRL 11 RQLEDIRLD 12 QLEDIRLDG 13 LEDIRLDGN 14 DEYFKRFNA 15 EYFKRFNAL 16 YFKRFNALQ 17 FKRFNALQY 18 KRFNALQYL 19 RFNALQYLR 20 FNALQYLRL 21 NALQYLRLS 22 ALQYLRLSH 23 LQYLRLSHN 24 QYLRLSHNE 25 LSHNEL 26 PLNLRSIDL 27 LNLRSIDLQ 28 NLRSIDLQD 29 LRSIDLQDF 30 RSIDLQDFF 31 SIDLQDFFS 32 IDLQDFFSS 33 DLQDFFSSL 34 LQDFFSSLI 35 DPCTTWCDA 36 RRRWRRLTV 37 ARGQPGVMG

(ii) MHC-Peptide Binding Assay:

Each peptide was screened for binding to HLAB*2705. Candidate peptides were assembled with B*2705 and analysed using the REVEAL™ MHC-peptide binding assay to determine their level of incorporation into MHC molecules. Binding to MHC molecules was compared to that of two known T-cell epitopes: a positive control peptide and an intermediate control peptide with very strong and weaker binding properties, respectively.

The binding score for each peptide is shown as a percentage relative to the binding of the positive control (see FIG. 6). Only peptides with scores ≧45% of this positive control are referred to as passed epitopes. This pass/fail threshold is shown graphically as the red line of FIG. 6. Passed peptide determinations are relative measures and thus served as a general guideline to binding affinity. In general, strong T-cell epitopes tend to be identified as clear positive responses in this assay. Binding of the intermediate control (yellow bar) is shown to allow comparison of sample peptides with another T-cell epitope with weaker binding characteristics in the assay.

Table 22 shows peptide binding results ordered by peptide I.D. number, while Table 23 shows peptide binding results ordered by highest score. Experimental standard error was obtained by triplicate positive and intermediate control binding experiments. The standard error for these controls is shown in Table 22 below and was assumed to be representative of the degree of error that would be present for all samples.

TABLE 22 Peptide binding results ordered by peptide I.D. number. Peptides with REVEAL ™ binding assay scores >45% are highlighted % Positive Peptide I.D. Control 1 105.51 2 5.26 3 0.72 4 0.24 5 0.43 6 0.00 7 0.04 8 0.04 9 0.02 10 1.06 11 0.50 12 0.00 13 2.17 14 0.06 15 0.48 16 0.47 17 0.15 18 106.17 19 1.20 20 1.81 21 0.11 22 0.13 23 0.55 24 0.50 25 0.03 26 0.00 27 0.11 28 0.17 29 0.08 30 0.08 31 0.26 32 0.13 33 0.35 34 0.11 35 2.18 36 43.98 37 0.00 Intermediate Control  30.33 +/− 0.3 Positive Control 100.00 +/− 3.8

TABLE 23 Peptide binding results ordered by highest binding score. Peptides with REVEAL ™ binding assay scores >45% are highlighted. Peptide I.D. % Positive Control Peptide I.D. Positive Control 18 106.17 21 0.11 1 105.51 27 0.11 Positive Control 100.00 +/− 3.8 34 0.11 36 43.98 30 0.08 Intermediate Control  30.33 +/− 0.3 29 0.08 2 5.26 14 0.06 35 7.18 7 0.04 13 2.17 8 0.04 20 1.81 25 0.03 19 1.20 9 0.02 10 1.06 12 0.00 3 0.72 26 0.00 23 0.55 37 0.00 24 0.50 6 0.00 11 0.50 15 0.48 16 0.47 5 0.43 33 0.35 31 0.26 4 0.24 28 0.17 17 0.15 22 0.13 32 0.13

Example 2 Role of Optican and Lumican Proteins in the Pathogenesis of Anterior Uveitis Materials and Methods (i) MHC Binding Assays

In a series of studies, the complete protein sequences of lumican, opticin and C. trachomatis were extracted from the Swiss-Prot database in a fasta format. Protein-sequences were analysed using the computational HLA-binding prediction software tools: SYFPEITHI (see Rada et al. (1993), “Regulation of corneal collagen fibrillogenesis in vitro by corneal proleoglycan (lumican and decorin) core proteins”, Exp Eye Res. 56(6): p. 635-48), and BIMAS (see Rammensee, et al., (1999), “SYFPEITHI: database for MHC ligands and peptide motit”, Immunogenetics. 50(3-4): p. 213-9). Using computational methods, 9-mer peptides that bound with variable affinities to HLA-B2705 (Table 24) were identified. This algorithm based method of detecting peptide binding can be inaccurate, may lead to both false positive and false negative results and cannot reveal which peptides are the most naturally immunogenic. Therefore we examined their binding affinity to HLA-B2705 with an in vitro MHC-peptide binding assay (REVEAL Epitope discovery system, Prolmmune, Oxford, UK) (see Rammensee, et al., (1999), supra). A total of 37 peptides derived from peptide sequences of interest from lumican, opticin and Chlamydia were tested. This strategy revealed that one of the original peptides (lumican peptide 1—Table 24) showed significant binding relative to the positive control peptides. It was subsequently ascertained if these peptides are recognised in vivo by T cells of patients with anterior uveitis (AU).

(ii) Patients

All subjects were recruited from the uveitis clinic at St Vincent's Hospital, Sydney. All patients had a detailed history and examination and were investigated as per our previously published protocol (see Burrows, et al., (2007), “The impact of HLA-B micropolymorphism outside primary peptide anchor pockets on the CTL response to CMV”, Eur J Immunol, 37(4): p. 946-53) and had serology performed for C. Trachomatis by Elisa. All patients with associated SpA were assessed by a rheumatologist or immunologist and fulfilled international diagnostic criteria for these diseases and fulfilled international diagnostic criteria for these diseases. Patients had HLA-B27 typing for stratification into study groups and their peripheral blood was collected for analysis. Patients on immunosuppressive therapy and biological agents (such as anti-TNF therapy) were excluded.

(iii) Immunohistochemistry

Human iris pigment epithelial (IPE) cell cultures, iris tissues and synovial tissues were stained with anti-lumican or control rabbit IgG, followed by HRP or Alexa-fluor conjugated goat anti-rabbit IgG as previously described.

(iv) Peptide Synthesis

Peptides were synthesized on an MK-IV peptide synthesizer, purified by HPLC and verified by liquid chromatography-mass spectrometry on an HPLC Shimadzu QP8000 system. All peptides were over 95% pure and stored at −20° C. until used. Peptides were dissolved in DMSO and stored at −80° C. until used.

(v) HLA Typing

HLA B27 typing was performed by flow cytometry and confirmed by PCR. DNA was extracted from PBMCs with the QlAamp kit (Qiagen); multiplex PCR analysis of this DNA (Dynal Biotech) was used for HLA-B2705 typing.

(vi) EliSpot Assay

PBMC from HLA-B27 patients with active disease and controls were tested with the selected peptides (Table 24) in ex vivo IFN-γ EliSpot assays as previously described (see Kuon and J Sieper, (2003), “Identification of HLA-B27-restricted peptides in reactive arthritis and other spondyloarthropathies: computer algorithms and fluorescent activated cell sorting analysic as tools for hunting of HLA-B27-restricted chlamydial and autologous crossreactive peptides involved in reactive arthritis and ankylosing spondylitis”, Rheum Dis Clin North Am, 29(3): p. 595-611; Glant, et al., (1988), “Mapping of arthritogenic/autoimmune epitopes of cartilage aggrecans in proteoglycan-induced arthritis”, Scand J Rheumatol Suppl, 101: p. 43-9; and Cantagrel, et al., (1988), “The transsynovial lymphocytic ratio. Characterization of blood and synovial fluid lymphocytes from patients with arthritic diseases”, J Rheumatol, 15(6): p. 899-904.)

Approximately 1×10⁵ PBMCs were used per well, with phytohemagglutinin or medium alone as the positive or negative control, respectively. Groups of three peptides were initially tested to ascertain which peptides stimulated a significant IFN-γ production. Each peptide or peptide combination was tested in triplicate at a concentration of 5 mM per peptide. This concentration of peptide was ascertained in preliminary studies to give optimal responses (data not shown). All positive responses were tested at lower peptide concentrations with cultured EliSpot assays of a subset of samples, where additional cells were available. Peptides found to bind to HLA-B2705 with high affinity (peptides 1, 6 and 7—Table 24) and low affinity binding peptides (peptides 2, 3, 4, 5, 8-10—Table 24), were included, as well as peptides know to stimulate T cells of patients with AS (peptide 8 and 9, Table 24) (see Kuon, W., et al., (1997), “Recognition of chlamydial antigen by HLA-B27-restricted cytotoxic T cells in HLA-B*2705 transgenic CBA (H-2k) mice” Arthritis Rheum, 40(5): p. 945-54).

Results (i) Patients

Twenty-five patients with HLA B27 related disease were examined. There were 17 males with a median aged 45.5 years and 8 females with a median age of 37.2 years. All patients were HLA B27 positive by flow cytometry.

(ii) Lumican Immunohistochemistry

Human IPE cultures (A and E), iris tissues (B and F), synovial tissues (C-D, G-H) were labelled with anti-lumican or control rabbit IgG, followed by HRP or Alexa-fluor conjugated goat anti-rabbit lgG. Lumican staining (red) is present in IPE in vitro (E) and in vivo (F), in blood vessels (bv) (G) and in articular cartilage (H) (FIG. 1).

(iii) Peptide Binding to HLA B2705

Predicted peptide binding to HLA-B2705 (ANN method) using tools from the Immune Epitope Database and Analysis Resource (see Appel, et al., (2004), “The solvent-inaccessible Cys67 residue of HLA-B27 contributes to T cell recognition of HLA-B27/peptide complexes”. J Immunol, 2004. 173(11): p. 6564-73) are shown in Table 24. IC₅₀ value <50 nM is considered to be high affinity, >5000 nM is considered to be low affinity. Reactivity to peptides derived from matrix components of the eye and joints (peptides 1-4 and 8-10—Table 24) and peptides derived from Chlamydia trachomatis (peptides 5-7—Table 24) were examined in patients with AU and relevant control subjects (Table 25). High and low affinity peptide sequences were included to serve as positive and negative controls.

TABLE 24 Nine-mer peptides and their predicted binding to HLA-B2705 Peptide IC₅₀ Accession Number Sequence Protein Origin (nM)^(#) number 1 KRFNALQYL Lumican 30.3 NP_002336.1 2 LQNNLIETI Keratocan/Opticin 2392.6 NP_008966.1 NP_055174.1 3 LQYLRLSHN Lumican 8955.5 NP_002336.1 4 QLEDIRLDG Opticin 28246.6 NP_055174.1 5 PLNLRSIDL Chlamydia trachomatis 26278.7 NP_219980.1 6 ARKLLLDNL Chlamydia trachomatis 267.8 NP_220127.1 7 NRFSVAYML I Chlamydia trachomatis 30.7 NP_219924.1 8 DRASFIKNL Collagen type VI alpha 2 (C34) 614.8 NP_478054.2 9 SRHHAFCFR Aggrecan 331.4 NP_001126.3 10 ARGQPGVMG Collagen type II alpha 1 13735.6 NP_149162.2 ^(#)Predicted peptide binding to HLA-B2705 (ANN method) using tools from the Immune Epitope Database and Analysis Resource. IC₅₀ value <50 nM is considered to be high affinity, >5000 nM is considered to be low affinity.

(iv) Chlamydia Serology

Thirteen of the 25 patients who participated in this study and one of the 6 control subjects had positive serology for C. Trachomatis as detected in an ELISA assay.

(v) EliSpot Assays

Mixtures were made into four groups of three peptides each, as shown in Table 25. An EBV-derived peptide was used as a standardisation control and whole recombinant human lumican was also used. The culture media (complete RPMI) was the negative control and PHA the positive control. 1×10⁵ cells were added per well, cells left to incubate for 24 hours and counted after the incubation of detection antibody and colour assay. Cells were then counted. For the purposes of data analysis values were normalised such that the number of counts in the negative control was defined as 1.0 and all other counts relative to this. Ten patients with HLA B27 AU were compared with healthy controls. These patients showed a significant difference between their response to lumican vs the average of the healthy controls (n=6) (one way ANOVA, Bonferroni multiple comparison test) (FIG. 3).

The response to individual peptide mixtures in two HLA B27 positive patients (b27028 and b27030) and two controls is shown in FIG. 2.

Table 25 outline IFN-γ EliSpot assay results from stimulation of PBMC with peptide mixtures and lumican protein. Patients with HLA B27 AU responded to peptides and lumican more frequently than controls (p<0.05) with 8 of 10 patients demonstrating increased IFN-γ production to lumican and (set 4) peptides derived from aggrecan, collagen and C. Trachomatis, and 6 of 10 patients responding to peptides derived from opticin and C. Trachomatis (set 2) peptides and interestingly to EBV peptides (Table 25).

TABLE 25 Interferon gamma response to HLA B27 binding peptides Patients Controls Set Peptide/protein Source (N = 10) (N-6) 1 KRFNALQYL Lumican 4 0 LQNNLIETI Keratocan/Opticin LQYLRLSHN Lumican 2 QLEDIRLDG Opticin 6 2 PLNLRSIDL Chlamydia trachomatis ARKLLLDNL Chlamydia trachomatis 3 NRFSVAYML Chlamydia trachomatis 1 1 KRLAETLAL Chlamydia trachomatis DRASFIKNL (Kuon) Collagen type VI alpha 2 (C34) 4 SRHHAFCFR Aggrecan 8 3 ARGQPGVMG Collagen type II alpha I IRSSVQNKL Chlamydia trachomatis EBV RRR... EBV restricted 6 1 Lumican Lumican Lumican 8 2

For 2 patients (B27004 and B27007) six different peptides were tested individually and one HLA B27 subject showed a significant increase in response compared to the controls (p<0.001, one way ANOVA, Bonferroni) fbr three of the peptides (LQNNLIETI (keratocan/opticin), LQYLRLSHN (lumican) and QLEDIRLDG (opticin)) (FIG. 4).

Peptides were divided into four groups based on source (aggrecan, lumican, opticin and Chlamydia trachomatis) as follows:

-   -   Lumican peptide mix: KRFNALQYL, LQYLRLSHN     -   Optican peptide mix: LQNNLIETI, QLEDIRLDG     -   Chlamydia peptide mix: PLNLRSIDL, ARKLLLDNL, NRFSVAYML     -   Collagen peptide: DRASFIKNL

Three HLA-B27 positive AAU patients and one HLA-B27 negative healthy control showed increased responses to the peptides from the patient compared to the control (FIG. 5).

Discussion

The data provided herein indicates that peptides derived from lumican, opticin and Chlamydia are able to bind HLA B2705 with high affinity and may have a role in the pathogenesis of HLA B27 related diseases.

This is the first study to implicate lumican and opticin in the pathogenesis of this group of HLA B27 related diseases. Lumican is an important SLRP, which is widely distributed in mammals. Immunohistochemical results provided herein show that lumican is expressed by iris pigment epithelial cells as well as iris tissue and cartilage. Lumican is also distributed in blood vessels and synovial joints. Thus the distribution of lumican is consistent with the distribution of inflammatory responses associated with HLA B27 diseases, such as the spondyloarthropathies (ankylosing spondylitis and reactive arthritis) and anterior uveitis.

Interestingly, HLA B27 patients showed positive interferon gamma responses to several of the peptides tested in these studies. In addition, they also showed response to lumican indicating that this protein and its peptides play a role in the pathogenesis of HLA B27 related diseases. As previously indicated, the distribution of this peptidoglycan is consistent with the localisation in HLA B27 diseases, which tend to involve synovial joints, cartilage and ocular tissue. Similarly opticin has not previously been implicated in the pathogenesis of these diseases—its distribution, particularly its ocular distribution, may explain disease localisation in patients with HLA B27 diseases. Previous studies have implicated Chlamydia trachomatis in the pathogenesis of HLA B27 diseases. This study provides evidence that molecular mimicry between C. trachomatis and specific peptide aequences in lumican and opticin may trigger an immune response leading to tissue damage in the characteristic pattern.

This study also shows that patients with HLA B27 acute anterior uveitis mount a T cell mediated immune response to lumican and that lumican has peptide sequences similar to those found in the outer membrane proteins of C. Trachomatis. It is postulated that molecular mimicry between lumican and C. Trachomatis outer membrane proteins may lead to an immune response generated by a preceding infection by C. trachomatis. It is hypothesised that inciting genital infection with C. trachomatis leads to a T cell mediated immune response that cross reacts with lumican and localises the inflammatory response in ocular and joint tissues, which is the characteristic pattern of disease observed in patients with SpAs and AU.

Example 3 Administration of Peptides to Lewis Rats

Animals: Lewis rats, age 6 weeks, day of immunization: 25.08.2011 Peptides were emulsified (sonification) in CFA (50:50, CFA:Peptid) supplemented with M Tuberculosis H37RA (BD, Heidelberg, Germany) to a final concentration of 2.5 mg/ml Peptide is injected s.c. in both hindlegs, 50 μg peptide/200 μl emulsion, 100 μl/leg, Group size: 6 animals, 3 groups

Group1 Peptide 1: KRFNALQYL Group 2 Peptide 2: ARKLLLDNL Group 3 Peptide 3: NRFSVAYML

7 days post immunization animals were examined daily (eyes and feet) In all groups, no clinical signs of inflammation were observed until day 25. On day 15 arthritis was first observed in Group 2 Gr. 1: very mild Arthritis in 2 rats, only observed on day 19/21 in animal 1 (hindleg, right), day 22 (hindleg r/l) Gr. 2: severe arthritis starting on day 15, animal 2-3,

Animal 1: day 19 H-left, day 22 H-left/right

Animal 2: no arthritis

Animal 3: day 15 H-left/right

Animal 4: very mild day 18 h-left, day 22 h-right, day 24 no arthritis Animal 5: very mild day 19, h-left Animal 6: severe day 15 h-left/right, day 18 forefoot-right, day 19 f-left

Gr. 3:

Animal 3: day 15 H-left, day 19 h-right. Animal 4: mild only on day 21 H-left/right Animals were sacrificed on day IS. Eyes were embedded in tissue tec and frozen at −80 degree. 8 μm cryo section were stained with hematoxilin and graded. Gr. 1: 1-1 l: ret fold (scoring 0.5)

-   -   1-2 r ret fold, −1-2 l: papillitis ? (scoring 0.5/0.5)         Gr. 2-2-3 r: papillitis (scoring 0.5)     -   2-5 r: papillitis—2-5 l: vasculitis? (Scoring (0.5/0.5)     -   2-6 r: ganglien cells (scoring 0.5)         Gr. 3-3-2 l: papillitis? (scoring 0.5)     -   3-3 r: gangl cells (scoring 0.5)

Summary T106

TABLE 26 peptide/ histol Arthritis Arthritis group animals peptide animal clin uveitis Average incidence Total day 25 1 6 Lew P1 50 μg 0 0.125 3/12 3 0 2 6 Lew P2 50 μg 0 0.181 5/11* 8 8 3 6 Lew P3 50 μg 0 0.083 2/12 4 2 *2-3 left eye, bad staining, no scoring

The three peptides above were generated and administered to mice. The mice were not HLA-B27 transgenics. Peptide 2 generated arthritis in 5/6 animals immunised. Two of these animals had quite severe arthritis in a pattern seen in this model with seronegative arthritis. In addition a group of 6 Lewis rats were immunised with Lumican and all developed arthritis. Preliminary results indicate that peptide 2 generates an arthritis that one would expect in a sero-negative type reactive arthritis.

Example 4 Induction of Oral Tolerance with the Peptides P2 (ARKLLLDNL) and P3 (NRFSVAYML) Materials and Methods

Rats were fed 3 times every other day with 200 Ctg peptide, the control groups received PBS. Three days after the last feeding rats were immunized with the respective peptides. One group was only immunized with CFA-emulsion as a control group for adjuvant arthritis. (see Table 27). Rats were observed daily for clinical evidence of uveitis or arthritis. Animals were euthenased after 3 weeks and histology performed on the eyes and joints of all animals.

Results

Peptide 3-P3 (NRFSVAYML) induces oral tolerance more effectively than P2 (Table 27).

None of the rats fed with P3 and immunized with P3 developed arthritis or uveitis. The results are summarized in Table 27.

Results show that rats immunized with peptide 3 (P3D7 ie Peptide 3 day 7) more often develop uveitis. With F148_4-3L (P3D7-fed, imm. P3D7) showed cells in the inner plexiform layer, some were apoptotic, F148_4-4R (P3D7-fed, imm. P3D7) has cellular infiltrates in the inner plexiform layer and F148_4-4L (P3D7-fed, imm. P3D7): perivascular infiltrate around a retinal vessel in the gaglion cell/inner plexiform layer. Only the left eye of rat 1-3 (F148_1-3L, PBS-fed, imm. P2D6) showed a big lesion of the posterior retina, reaching the inner nuclear layer, thus resulting in a histological score of 2-3 for affecting a large region of the retina.

All effected joints showed evidence of acute inflammation and synovitis. None of the animals who received P3 had evidence of arthritis or uveitis.

TABLE 27 Summary of oral tolerance experiments Immunized affected average Group/animals oral tolerogen with incidence joints score/animal 1/ PBS 0.5 ml 3 x 100 μg P2 100 μl/ 2/4 3 1.875 4 rats hindleg 2/ P2 (ARKLLLDNL) 200 μg/0.5 ml 3 x 100 μg P2 100 μl/ 1/4 4 + tail 3.25 4 rats PBS hindleg (2.?) (2x) 3/ PBS 0.5 ml 3 x 100 μg P3 100 μl/ 3/4 10  2.75-3.00 4 rats hindleg 4/ P3 (NRFSVAYML) 200 μg/0.5 ml 3 x 100 μg P3 100 μl/ 0/4 0 0 4 rats PBS hindleg 5/ □ CFA 100 μl/ 1/4 2 1 4 rats hindleg

Example 5 Serology of Chlamydia trachomatis Materials and Methods

Serology studies were undertaken using a recombinant enzyme-linked inmmunosorbant assay (ELISA) for the quantitative detection of specific IgG to genus-wide chlamydial LPS in human serum. This is based on an exclusively Chlamydia-specific fragment from the LPS which has not been found in any other bacterial LPS.

Sera were diluted 1:100 with sample diluent. 50 μL of the negative control, positive control and the diluted patient samples were pipetted in duplicate into the wells of the 96 well microplate as well as sample diluent as blank. The microplate wells were incubated for 60 minutes (37 C.°, 5% CO₂). After incubation the microplate wells were washed three times with 200 μL wash buffer per well. After washing the microplate was tapped on filter paper. 50 μL conjugated antibody was pipetted into each well and allowed to incubated for 60 minutes (37 C.°, 5% CO₂). After incubation the wells were washed three times with 200 μL wash buffer per well and the microplated tapped on filter paper. 50 μL TMB-substrate was added per well and the microplate was allowed to incubate in the dark for 30 minutes (37 C.°, 5% CO₂). Positive samples turn blue. The reaction was subsequently stopped with the addition of 100 μL stop solution per well.

Results

165 patients with anterior uveitis (AU) were examined of whom 31% had positive serology (25% HLAB27+ve and 41% HLAB27−ve), this is significantly higher than the community control population.

Example 6 Peptide-specific CD4+ T cells (Chlamydia and Lumican) in HLAB2+ Patients Materials and Methods

A protocol involving whole blood was used to examine the activated CD4+ and CD8+ T cell responses to antigens (peptides 1-7: see Table 28). With respect to examining the activation of CD4+ T cell responses, the protocol was developed based on the method developed by Zaunders et al. (Zaunders et al., 2009, “High levels of human antigen-specific CD4+ T cells in peripheral blood revealed by stimulated coexpression of CD25 and CD134 (OX40)”, J. Immunol. 183(4): 2827-36). This involves stimulating whole blood with antigen (peptide) or mitogen and then measuring cell surface expression of CD25 and CD134 (OX40). In order to determine the activity of CD8+ T cells the expression of cell surface markers CD25, CD38, CD137 and HLA-DR were measured.

Whole blood was collected in lithium-heparin vacutainer tubes. 250 μL of blood was transferred to a well in a 24-well plate and mixed with an equal amount of culture media. Antigens were added and the plate was allowed to incubate for 40-48 hours (37° C., 5% CO₂). After incubation, 200 μL blood/media mixture was transferred from each well into two separate 12×75 mm FACS tubes. One tube would be used to stain with antibodies examining CD4 activation, while the other would be stained with antibodies examining CD8 activation. Antibodies for each panel were mixed together. The antibody mixture was added to each tube. Once antibody was added the tube was gently vortexed and allowed to incubate for 15 minutes at room temperature in the dark. 2 mL FACS lysing solution was then added, gently vortexed and incubated for ten minutes at room temperature in the dark. After centrifugation (300 g, 5 minutes), supernatant was decanted followed by a wash with 2 mL wash buffer. After supernatant was decanted 350 μL BD PBS was added and stored at 2 -8° C. in the dark until analysed on FACS Flow Cytometer. The negative control was whole blood in media without any antigen. Staphylococcal enterotoxin B (SEB), a superantigen, was used as a positive control.

Results

The data shows that patients have peptide-specific CD4+ T cells in their peripheral blood to the Chlamydia peptides. These results show that 50% of the HLAB27 patients with AU have CD4+ T cells that recognise the respective Chlamydia and Lumican peptides (FIG. 8). These correspond to the patients with positive serology. The responding CD4+ T cells are in low concentration in peripheral blood and would be expected to be in higher concentrations in the inflamed ocular tissue.

TABLE 28 Sequences of peptide antigens administered to blood of HLAB27+ patients Peptide No. Sequence Peptide Source 1 KRLAETLAL Chlamydia trachomatis 2 ARKLLLDNL Chlamydia trachomatis 3 IRSSVQNKL Chlamydia trachomatis 4 KRFNALQYL Human Lumican 5 LQYLRLSHN Human Lumican 6 NRFSVAYML Chlamydia trachomatis 7 PLNLRSIDL Chlamydia trachomatis Lumican Human Lumican Protein Human Lumican Protein 

1. An isolated polypeptide comprising a sequence of at least six amino acid residues, wherein said sequence shares at least 65% sequence homology with: (a) a mammalian small leucine-rich repeat protein/proteoglycan (SLRP) polypeptide sequence; and (b) a polypeptide sequence from an infectious microorganism, wherein said SLRP is selected from lumican, opticin and keratocan.
 2. The isolated polypeptide of claim 1, wherein said isolated polypeptide is: (i) 12 amino acid residues or less in length, or (ii) 9 amino acid residues in length.
 3. (canceled)
 4. The isolated polypeptide of claim 1, wherein the infectious microorganism is from a species in genus Chlamydia or Aspergillus.
 5. The isolated polypeptide of claim 1, wherein the polypeptide sequence of (b) comprises SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 36, SEQ ID NO: 37, or SEQ ID NO:
 38. 6. The isolated polypeptide of claim 1, wherein the polypeptide sequence of (a) comprises: (i) residues 222-275 of the amino acid sequence set forth in SEQ ID NO: 1; (ii) residues 222-247 of the amino acid sequence set forth in SEQ ID NO: 1: (iii) residues 222-241 of the amino acid sequence set forth in SEQ ID NO: 1; (iv) residues 264-315 of the amino acid sequence set forth in SEQ ID NO: 30; or (v) 264-315 of the amino acid sequence set forth in SEQ ID NO:
 32. 7.-8. (canceled)
 9. The isolated polypeptide claim 1, wherein said sequence of at least six amino acid residues comprises: (i) SEQ ID NO: 2 (KRFNALQYL); (ii) a variant of SEQ ID NO: 2 (KRFNALOYL) comprising at least one amino acid substitution; (iii) a fragment of SEQ ID NO: 2 (KRFNALOYL); or (iv) SEQ ID NO: 34 (LOYLRLSHN).
 10. (canceled)
 11. The isolated polypeptide of claim 9, wherein said variant is selected from the group consisting of KRFNALQCL (SEQ ID NO: 3), KRFNALQLL (SEQ ID NO: 4), and a fragment thereof.
 12. (canceled)
 13. The isolated polypeptide of claim 9, wherein said fragment is selected from a sequence set forth in any one of SEQ ID NOs: 9-17.
 14. The isolated polypeptide of claim 11, wherein said polypeptide comprises a fragment of KRFNALQCL (SEQ ID NO: 3) or KRFNALQLL (SEQ ID NO: 4) selected from a sequence set forth in any one of SEQ ID NOs: 18-29. 15.-16. (canceled)
 17. The isolated polypeptide of claim 1, wherein said sequence of at least six amino acid residues comprises SEQ ID NO: 31 (LQNNLIETM) or SEQ ID NO: 35 (QLEDIRLDG).
 18. (canceled)
 19. The isolated polypeptide of claim 1, wherein said sequence of at least six amino acid residues comprises SEQ ID NO: 33 (LQNNLIETI).
 20. The isolated polypeptide of claim 1, wherein the binding affinity of said sequence of at least six amino acid residues to human leukocyte antigen B27 (HLA-B27) as measured by IC₅₀ value is less than about 500 nm.
 21. A pharmaceutical composition comprising the isolated polypeptide of claim
 1. 22. The pharmaceutical composition of claim 21, wherein said composition is a preventative or therapeutic vaccine.
 23. A method for preventing or treating an HLA-B27-associated autoimmune disease in a subject, the method comprising administering to the subject a therapeutically effective amount of the isolated polypeptide of claim 1, or the pharmaceutical composition of claim
 21. 24. A method for determining a predisposition to developing an HLA-B27-associated autoimmune disease in a subject, the method comprising: contacting a biological sample from the subject with the polypeptide of claim 1; and detecting the presence or absence of an immune cell or antibody specific for said polypeptide in the biological sample, wherein detection of said immune cell or antibody is indicative of a predisposition to developing said disease.
 25. A method for diagnosing an HLA-B27-associated autoimmune disease in a subject, the method comprising: contacting a biological sample from the subject with the polypeptide of claim 1; and detecting the presence or absence of an immune cell or antibody specific for said polypeptide in the biological sample, wherein detection of said immune cell or antibody is indicative of a predisposition to developing said disease.
 26. The method of claim 24, comprising the additional step of determining the human leukocyte antigen type (HLA-type) of the subject.
 27. The method of claim 24, wherein said detecting comprises: (i) analysing antibody binding by enzyme-linked immunosorbent assay (ELISA), (ii) analysing cell proliferation, (iii) analysing cytokine synthesis, or (iv) analysing cell surface marker expression.
 28. The method according to claim 23, wherein the HLA-B27-associated autoimmune disease is a spondyloarthropathy selected from the group consisting of ankylosing spondylitis, psoriatic arthritis, undifferentiated spondyloarthropathy, juvenile onset spondyloarthropathy, enteropathic arthritis, arthritis mutilans, reactive arthritis (Reiter's syndrome), reactive arthritides, sacroiliitis, spondylitis of inflammatory bowel disease, Crohn's disease associated with spondyloarthropathy, whipple disease, anterior uveitis, and Behcet disease.
 29. (canceled) 